Integrated proteomics and single-cell transcriptomics reveal immune dynamics and severity markers in acute Plasmodium falciparum malaria

Set up

Load libraries

library(tidyverse)
library(readxl)
library(DT)
library(Matrix)
library(patchwork)
library(gridExtra)
library(viridis)
library(RColorBrewer)
library(ComplexHeatmap)
library(circlize)
library(purrr)
library(broom)
#library(broom.mixed)
library(igraph)
library(ggpubr)
library(correlation)
library(ggrepel)
library(ggalluvial)
library(Seurat)
library(clusterProfiler)
library(umap) ## https://github.com/tkonopka/umap/blob/master/vignettes/umap.Rmd
library(tidygraph)
library(ggraph)
library(scales)
library(WGCNA)
library(mixOmics)
library(eulerr)
library(lmerTest)
#library(broom.mixed)
library(emmeans)

Load data

# Malaria Explore 1536 data
data <- utils::read.delim("../data/data/explore1536/20230411_infectious_olink.tsv") 
# Malaria sampleTable
sampleTable_simple <- readRDS("../data/metaData_clean/Explore1536_Malaria_sampleTable_simple.rds")
# Malaria subjectTable
subjectTable <- readRDS("../data/metaData_clean/MalariaResource_subjectTable.rds")
# Malaria clinchem data
clinchem_study_pats_acute.wide <- readRDS("../data/metaData_clean/Explore1536_ClinicalChemistry_acute.rds")

# Tropical fever Explore 1536 data
TF.long <- readRDS("../data/data_clean/Explore1536_TF_tidy_long.rds")
# Tropical fever sampleTable
TF_sampleTable <- readRDS("../data/metaData_clean/Explore1536_TF_sampleTable.rds")


# HPA v24
hpa_24.0 <- read_tsv("../data/hpa/proteinatlas_v24.tsv") %>% janitor::clean_names() %>% 
  mutate(secretome_location = ifelse(is.na(secretome_location),"Not secreted",secretome_location))
# HPA tissue expression v23
hpa.tissue <- read_tsv("../data/hpa/rna_tissue_consensus.tsv") %>% janitor::clean_names()


# Load cleaned malaria data
#-   assays with QC warn in more than 70% of all assays
#-   samples with more than 70% below LOD
data.wide <- readRDS("../data/data_clean/Explore1536_tidy_wide.rds")
data.long <- readRDS("../data/data_clean/Explore1536_tidy_long.rds")

## Explore 1536 data set - MGH Covid-19 study, Filbin et al. 2021
covid_NPXdata <- read_delim("../data/MGH_OLINK_COVID/MGH_COVID_OLINK_NPX.txt",comment = "##")
mgh.covid.meta <- read_delim("../data/MGH_OLINK_COVID/MGH_COVID_Clinical_Info.txt", comment="##") %>% janitor::clean_names()
mgh.covid.meta.key <- read_excel("../data/MGH_OLINK_COVID/variable_descriptions.xlsx")

## load tropical fever cohort data
TF_SOFA <- readRDS("../data/metaData_clean/2021213_TF_DA_TROP_SOFAscores.rds") %>% filter(diagnose_clean!="P.falciparum")
TF.long <- readRDS("../data/data_clean/Explore1536_TF_tidy_long.rds")

## loding  MIP Cohort FACS data - Lautenbach et al. Cell Reports 2022

FACs_data <- read_delim("../../MalariaTravellers/data/TravellerCohort_FACS_log2cpu_long.csv")
FACS_meta <- read_delim("../../MalariaTravellers/data/TravellerCohort_SubjectTable.csv")

Set theme & colors

theme_set(theme_minimal(base_size = 6))

time3_col <- c("Acute" = "#C51B7D", 
               "D10" = "#E9A3C9",
               "M12" = "#4D9221")

sex2_col <- c(male = "#c5b8dc",
              female = "#b9d2b1")

endemic2_col <- c(primary_infected = "#998EC3",
                  previously_exposed = "#F1A340")
severe_5_col = c("1"="tomato",
                 "0"="grey80")

secretome_location_cols <- c("Secreted to blood" = "#FB8072",
                             "Intracellular and membrane" = "#8DD3C7",
                             "Secreted in other tissues" = "#B3DE69",
                             "Secreted to extracellular matrix" = "#80B1D3",
                             "Secreted in brain" = "#b9d2b1",#"#FCCDE5",
                             "Secreted to digestive system" = "#FDB462",
                             "Secreted - unknown location" = "#FFFF00",
                             "Secreted in male reproductive system" = sex2_col[[1]],#"#BEBADA",
                             "Secreted in female reproductive system" = sex2_col[[2]],
                             "Not secreted" = "#D9D9D9")

secretome_location_tissue_spec_cols <- c(secretome_location_cols,
                                         c("Not secreted - Tissue enriched" = "#88419d",
                                           "Not secreted - Tissue enhanced" = "#8c96c6",
                                           "Not secreted - Group enriched" = "#b3cde3",
                                           "Not secreted - Low tissue specificity" = "#edf8fb")
                                         )

SOFA_sub_col = colorRamp2(c(0,4), c("white","red"))

patient_kclust3 <- c('3' = "#92c5de", '2' = "#f4a582", '1' = "#ca0020")
patient_kclust3_lab <- c("mild"="#92c5de", "moderate"="#f4a582", "severe"="#ca0020")
patient_kclust3_lab_conv <- c("mild"="#92c5de", "moderate"="#f4a582", "severe"="#ca0020","convalescence" ="grey50")



SOFA_sub_col = colorRamp2(c(0,4), c("white","red"))

SOFA_total_col = colorRamp2(c(min(subjectTable$SOFA_total,na.rm = TRUE),
                              median(subjectTable$SOFA_total,na.rm = TRUE),
                              max(subjectTable$SOFA_total,na.rm = TRUE)),
                            c(brewer.pal(3,name="PuBu")))

## dimensinality reduction theme
my_dimred_theme <- theme_classic() + 
  theme(axis.text = element_blank(),
        axis.ticks = element_blank(),
        #text = element_text(size = 12),
        #legend.text = element_text(size = 10),
        legend.position = "right") 

## a4 pdf theme
theme_a4_pdf <- theme(axis.text.x = element_text(size=6),
                      axis.text.y = element_text(size=6),
                      axis.title.x = element_text(size=6),
                      axis.title.y = element_text(size=6),
                      ## legend
                      legend.key.size = unit(1, 'cm'), #change legend key size
                      legend.key.height = unit(0.25, 'cm'), #change legend key height
                      legend.key.width = unit(0.25, 'cm'), #change legend key width
                      legend.title = element_text(size=6), #change legend title font size
                      legend.text = element_text(size=6),
                      ## label
                      plot.title = element_blank(),
                      plot.subtitle =  element_blank(),
                      plot.caption =  element_blank(),
                      ## facet_grid
                      strip.text.x = element_text(size = 6,face="bold"),
                      #strip.text.y = element_text(size = 6),
                      strip.placement = "outside"
)

## patchwork panel a4 pdf theme
patchwork_panel_a4_pdf <- patchwork::plot_annotation(theme = theme(plot.title = element_text(size = 12),
                                                                   plot.tag = element_text(size = 16,face = 'bold')
),
tag_levels = 'A') 

asym_study_id <- c("2021004")

## 2013004 - Lib 1
## 2013007 - Lib 2
## 2013008 - Lib 3
## 2018002 - Lib 4

rhapsody_study_ids <- c("2013004","2013007","2013008","2018002")

#require(clusterProfiler)

#length(unique(data$UniProt)) ## 1463
mapping_uniprot_ensembl <- bitr(unique(data$UniProt), 
                                fromType="UNIPROT",
                                toType=c("SYMBOL", "ENSEMBL","ENTREZID"), 
                                OrgDb="org.Hs.eg.db") %>% 
  dplyr::rename(UniProt = UNIPROT,
                Symbol = SYMBOL,
                Ensembl = ENSEMBL,
                Entrez = ENTREZID) %>%
  inner_join(data %>% dplyr::select(Assay,UniProt) %>% dplyr::distinct(),by="UniProt")

#write_delim(mapping_uniprot_ensembl, "../../2022_Explore1536FarnertLab/data/Mapping_Explore_UniProt2Ensembl.txt")

Figure 1

Plasma proteomic perturbation during clinical malaria - Cohort characteristics

fig1.list <- list()

Figure 1B

(fig1.list[["general_sex_age_dist"]] <- subjectTable %>% 
    ggplot(aes(x=age, fill=sex)) +
    geom_density(alpha=.6) +
    #theme_classic() +
    theme(axis.text = element_text(size=6), 
          axis.title = element_text(size=6), 
          axis.ticks.x = element_blank()) + 
    scale_fill_manual(values=sex2_col) +
    scale_color_manual(values=sex2_col) +
    
    labs(fill="Sex",
         x="age [years]",
         y="density")
)

Figure 1C

(fig1.list[["timepoint_sex_perc"]] <-sampleTable_simple %>% 
    inner_join(subjectTable,by="study_id") %>% 
    group_by(Time,sex) %>% 
    tally() %>% 
    group_by(Time) %>% 
    dplyr::mutate(percent=n/sum(n)) %>% 
    ggplot(aes(x=Time,y=n,fill=sex)) +
    geom_bar(stat="identity", position ="fill") +
    geom_text(aes(label=paste0(sprintf("%1.1f", percent*100),"%")),
              position=position_fill(vjust=0.5), colour="white", size =1.5) +
    scale_y_continuous(labels = scales::percent,expand = c(0,.01)) + 
    #theme_minimal() +
    theme(legend.position = "top",
          axis.ticks.x = element_blank()) + 
    scale_fill_manual(values=sex2_col) +
    labs(fill=NULL,
         x=NULL,
         y="Percentage")
)

Figure 1D

(fig1.list[["timepoint_exposure"]] <- sampleTable_simple %>% 
    inner_join(subjectTable,by="study_id") %>% 
    group_by(Time,endemic) %>% 
    tally() %>% 
    group_by(Time) %>% 
    dplyr::mutate(percent=n/sum(n)) %>% 
  mutate(endemic = factor(endemic, levels=c("primary_infected","previously_exposed"))) %>% 
    ggplot(aes(x=Time,y=n,fill=endemic)) +
    geom_bar(stat="identity", position ="fill") +
    geom_text(aes(label=paste0(sprintf("%1.1f", percent*100),"%")),
              position=position_fill(vjust=0.5), colour="white", size =1.5) +
    scale_y_continuous(labels = scales::percent,expand = c(0,.01)) + 
    #theme_minimal() +
    theme(legend.position = "top",
          axis.ticks.x = element_blank()) + 
    scale_fill_manual(values=endemic2_col,labels=c("primary_infected"="primary infected","previously_exposed"="previously exposed")) +
    labs(fill=NULL,
         x=NULL,
         y="Percentage")
)

Figure 1E

df <- data.wide %>% 
  inner_join(sampleTable_simple %>% 
               transmute(sample_id),
             by="sample_id") %>% 
  column_to_rownames("sample_id")

## PC calculation
pcaRes <- stats::prcomp(df,center = TRUE, scale. = TRUE)
varExp <- round(pcaRes$sdev^2 / sum(pcaRes$sdev^2) * 100)
pcaDF <- data.frame(PC1 = pcaRes$x[, 1],
                    PC2 = pcaRes$x[, 2]) %>% 
  rownames_to_column("sample_id") 

## Prep for plotting
data4plot <- pcaDF %>% 
  dplyr::inner_join(sampleTable_simple, by="sample_id")


(pca_fig1 <- data4plot %>% 
    ggplot(mapping = aes(x = PC1, y = PC2, color = Time,fill=NULL, label = NULL)) +
    geom_point(alpha = 0.9, size = 1) +
    ggplot2::scale_color_manual(values= time3_col) +
    labs(x = paste0("PC1 (",  varExp[1], " %)"),
         y = paste0("PC2 (",  varExp[2], " %)")) +
    theme_minimal()  +
    theme(legend.title = element_text(size = 6), 
          legend.text = element_text(size = 6)))

Figure 1F

## nest data
data_nested <- data.long %>% 
  inner_join(sampleTable_simple, by="sample_id") %>% 
  group_by(UniProt,Assay) %>% 
  nest()

## nest data
data_nested <- data.long %>% 
  inner_join(sampleTable_simple, by="sample_id") %>% 
  left_join(subjectTable %>% transmute(study_id, 
                                       exposure = factor(endemic, levels=c("primary_infected","previously_exposed"))),
            by="study_id") %>% 
  group_by(UniProt,Assay) %>% 
  nest()

lme_res <- data_nested %>% 
  mutate(lme.res.simple = purrr::map(data, ~ lmerTest::lmer(NPX ~ Time + exposure + (1|study_id), REML = F,
                                                            control = lme4::lmerControl(check.conv.singular = "ignore"),
                                           data = .x %>% dplyr::filter(Time!="D10"))),
         lme.res.complex = purrr::map(data, ~ lmerTest::lmer(NPX ~ Time * exposure + (1|study_id), REML = F,
                                                             control = lme4::lmerControl(check.conv.singular = "ignore"),
                                           data = .x %>% dplyr::filter(Time!="D10"))),
         lme.simple.tidy = purrr::map(lme.res.simple, ~ broom.mixed::tidy(.,)),
         lme.complex.tidy = purrr::map(lme.res.complex, ~ broom.mixed::tidy(.)),

         posthoc.time = purrr::map(lme.res.simple, ~ summary(contrast(emmeans(., ~ Time), method = "pairwise")) %>% tibble()),
         posthoc.time_exposure = purrr::map(lme.res.complex, ~ summary(contrast(emmeans(., ~ Time * exposure), method = "pairwise")) %>% tibble())
         )

• finding better model

## compare simple (without interaction) with complex model (interaction)
bic_aic_res <- lme_res %>% 
  mutate(simple_glance = purrr::map(lme.res.simple, ~(broom::glance(.))),
         complex_glance = purrr::map(lme.res.complex, ~(broom::glance(.)))) %>% 
  unnest(cols = c(simple_glance,complex_glance),names_sep = ".") %>% 
  dplyr::select(Assay, contains("AIC"),contains("BIC"))

df_better_model <- bic_aic_res %>% 
  pivot_longer(cols=c(-UniProt,-Assay)) %>% 
  separate(name, into=c("model","eval"),sep = "\\.",remove = T) %>% 
  pivot_wider(names_from = model, values_from = value) %>% 
  mutate(simple_better = simple_glance < complex_glance,
         simple_delta = simple_glance-complex_glance,
         better_model = case_when(abs(simple_delta)>6 ~ "complex",
                                  .default = "simple"))

df_better_model %>% 
  group_by(eval) %>% 
  count(better_model) %>% 
  ggplot(aes(x=better_model, y=n)) +
  geom_col() +
      geom_text(aes(label=n),size=2,nudge_y = 50) + 
  facet_wrap(~eval)

df_better_model %>% filter(eval=="BIC",
                           better_model=="complex") 

## # A tibble: 14 × 8
## # Groups:   UniProt, Assay [14]
##    UniProt Assay   eval  simple_glance complex_glance simple_better simple_delta
##    <chr>   <chr>   <chr>         <dbl>          <dbl> <lgl>                <dbl>
##  1 Q9Y275  TNFSF1… BIC           276.           267.  FALSE                 9.66
##  2 P10586  PTPRF   BIC           153.           146.  FALSE                 7.56
##  3 P05107  ITGB2   BIC           148.           141.  FALSE                 6.98
##  4 Q9HAN9  NMNAT1  BIC           401.           394.  FALSE                 6.73
##  5 P50135  HNMT    BIC           340.           332.  FALSE                 8.39
##  6 Q9UL46  PSME2   BIC           199.           192.  FALSE                 6.96
##  7 P04179  SOD2    BIC           328.           319.  FALSE                 9.55
##  8 P00352  ALDH1A1 BIC           302.           290.  FALSE                11.6 
##  9 Q9P0V8  SLAMF8  BIC           308.           301.  FALSE                 6.78
## 10 Q16772  GSTA3   BIC           350.           341.  FALSE                 8.69
## 11 Q86SF2  GALNT7  BIC            74.3           68.0 FALSE                 6.33
## 12 Q96I15  SCLY    BIC           280.           273.  FALSE                 6.67
## 13 Q00796  SORD    BIC           401.           391.  FALSE                10.3 
## 14 Q7Z4W1  DCXR    BIC           300.           289.  FALSE                11.3 
## # ℹ 1 more variable: better_model <chr>

lme_res_padj <- lme_res %>% 
  unnest(cols="posthoc.time") %>% 
  filter(contrast=="Acute - M12") %>% 
  ungroup() %>% 
  mutate(p.adj = p.adjust(p.value, method="fdr"),
                  FDR = ifelse(p.adj <= 0.01, TRUE,FALSE)) %>% 
  arrange(p.adj)

assay_better_complex_model <- df_better_model %>% filter(eval=="BIC",
                                                         better_model=="complex") %>% pull(Assay)

plot(euler(
  list("acute_m12" = lme_res_padj %>% filter(FDR==T) %>% pull(Assay),
       "bic_complex_better" = assay_better_complex_model)),#df_better_model %>% filter(eval=="BIC", better_model=="complex") %>% pull(Assay))),
  
        fills = c("#C51B7D",
                  "white"),
       quantities = TRUE,
       lty = 1,#1:3,
       fontsize=2,
       labels = list(fontsize=7),
       shape = "ellipse",adjust_labels = T)

lme_res_padj %>% 
  transmute(Assay, estimate,p.adj) %>% 
  filter(Assay %in% assay_better_complex_model) %>% 
  arrange(-abs(estimate))

## # A tibble: 14 × 3
##    Assay    estimate    p.adj
##    <chr>       <dbl>    <dbl>
##  1 SLAMF8     2.48   4.64e-16
##  2 HNMT       1.42   2.76e- 7
##  3 NMNAT1     1.18   1.77e- 3
##  4 ALDH1A1    1.13   3.00e- 6
##  5 TNFSF13B   1.04   1.30e- 6
##  6 GSTA3      1.03   5.20e- 4
##  7 SOD2       0.920  5.69e- 4
##  8 SCLY       0.905  1.54e- 5
##  9 PSME2      0.814  6.65e- 8
## 10 DCXR       0.637  3.36e- 3
## 11 ITGB2      0.623  2.43e- 8
## 12 SORD       0.391  3.10e- 1
## 13 GALNT7    -0.0573 4.89e- 1
## 14 PTPRF     -0.0129 9.28e- 1

dap.res <- lme_res_padj %>% 
  dplyr::rename(logFC = estimate) %>% 
  mutate(direction = ifelse(logFC<0,"down","up"))  %>% 
  dplyr::select(-c(lme.res.simple,lme.res.complex,lme.complex.tidy)) %>% 
  ## remove assays that would require a complex model
   filter(!Assay %in% assay_better_complex_model)

(dap.acute.volcano <- dap.res %>% 
   ggplot(aes(x=logFC, y=-log10(p.adj), color=FDR)) +
   geom_point(alpha=0.7,size=.5, shape=16) +
   theme_minimal() +
   ggrepel::geom_text_repel(data = . %>% filter(FDR ==TRUE, abs(logFC) >1.5),
                            aes(label = Assay), color="black",
                            force        = 0.5,
                            direction    = "both",
                            segment.size = 0.2,
                            segment.alpha=.1,
                            show.legend = F,
                            size=1,
                            max.overlaps = 16,
                            box.padding = unit(0.2, "lines"),
                            point.padding = unit(0.5, "lines"),
                            segment.color = 'grey50') +
   
   geom_vline(xintercept = c(-1, 1), linetype = "dotted", size = .5) +
   geom_hline(yintercept = -log10(0.01), linetype = "dotted", size = .5) + 
   #scale_x_continuous(breaks=c(-5.0,-2.5,-1.0,0.0,1.0,2.5,5.0,7.5),limits = c(-5,7.5)) +
      scale_x_continuous(breaks=c(-4.0,-3.0,-2.0,-1.0,0.0,1.0,2.0,3.0,4.0,5.0,6.0),limits = c(-4,6)) +

   geom_segment(aes(x = 1.1, y = 21, xend = 4, yend = 21), color=time3_col[[1]], #y=16.5
                arrow = arrow(length = unit(0.2, "cm"))) +
   annotate("text",x=2.6, y=22.5, size=2, label="High abundant\nin acute malaria") + #y=17.6
   
   geom_segment(aes(x = -1.1, y = 21, xend = -4, yend = 21),color=time3_col[[1]],
                arrow = arrow(length = unit(0.2, "cm"))) +
   annotate("text",x=-2.6, y=22.5, size=2, label="Low abundant\nin acute malaria") + #y=17.1
   
   labs(x="Estimated difference (NPX) at acute compared to convalescence",
        y="-log10(adj. p-value)") +
   theme(legend.position = "none",
         text = element_text(size=6)) +
   scale_color_manual(values= c(time3_col[[3]],time3_col[[1]])))

Figure 1G

hm.input <- data.wide %>% 
  inner_join(sampleTable_simple %>% dplyr::select(DAid,study_id, sample_id, Time),by="sample_id") %>% 
  dplyr::filter(Time=="Acute")

top25 <- dap.res %>% dplyr::filter(FDR==TRUE) %>%
  arrange(desc(abs(logFC)),desc(p.adj)) %>%
  mutate(up_down = ifelse(logFC>0,"up","down")) %>% 
  dplyr::group_by(up_down) %>% 
  slice_head(n=25)

top25.split <- top25 %>% column_to_rownames("Assay") %>% transmute(direction = factor(direction, levels = c("up","down"), labels = c("high","low")))

norm.df <- hm.input %>% column_to_rownames("sample_id") %>% 
  dplyr::select(-c(DAid,Time,study_id)) %>% 
  dplyr::select(c(top25$Assay)) %>% 
  t() %>% scale()

## == ComplexHeatmap == ##
(acute.npx.top25.hm <- norm.df %>% 
    scale() %>% 
    Heatmap(name="scaled\nNPX",
            clustering_distance_columns = "spearman",
            clustering_method_columns="ward.D2",
            
            top_annotation = HeatmapAnnotation(df = data.frame(sample_id = colnames(.)) %>%
                                                 separate(sample_id, into = c("study_id","Time"),sep="\\|") %>% 
                                                 left_join(subjectTable %>% transmute(study_id,
                                                                                      endemic = factor(case_when(endemic=="primary_infected"~"primary",
                                                                                                          endemic=="previously_exposed"~"previously",
                                                                                                          .default=NA),levels=c("primary","previously")),
                                                                                      severe_5 = ifelse(severe_5==1,"yes","no"))) %>%
                                                 dplyr::select(-study_id,-Time),
                                               simple_anno_size = unit(2, "mm"),
                                               show_annotation_name = F,
                                               annotation_legend_param = list(labels_gp = gpar(fontsize = 6),
                                                                              title_gp = gpar(fontsize = 6),
                                                                              legend_height = unit(3, "mm"), 
                                                                              grid_width = unit(3, "mm")),
                                               show_legend = T,
                                               annotation_label = list(severe_5 = "Severe malaria\n(WHO)",
                                                                       endemic = "exposure"),
                                        col = list(endemic =  c("previously"= "#F1A340","primary"= "#998EC3"),#endemic2_col,
                                                   severe_5 = c("yes"="tomato","no"="grey80")),#severe_5_col),
                                        which="column"),
            
            show_column_names = F,
            column_names_gp = gpar(fontsize = 8),
            show_column_dend = TRUE,
            cluster_columns = TRUE,
            column_dend_reorder = TRUE,
            row_dend_reorder=1-rowSums(abs(norm.df)),
            cluster_row_slices = FALSE,
            row_dend_width = unit(0.5, "cm"), 
            column_dend_height = unit(0.5, "cm"), 
            raster_resize_mat = mean,
            row_title_gp = gpar(fontsize=6),
            show_row_names = TRUE,
            row_split = top25.split,
            row_gap = unit(0.05,"cm"),
            row_names_gp = gpar(fontsize = 6),
            heatmap_legend_param = list(labels_gp = gpar(fontsize = 6),
                                        title_gp = gpar(fontsize = 6),
                                        legend_height = unit(3, "mm"), 
                                        grid_width = unit(3, "mm")),
            height = ncol(.)*unit(1.4, "mm"),
            width = ncol(.)*unit(.14,"mm")
    ))

Figure 1H

top10up <- dap.res %>% dplyr::filter(FDR==TRUE) %>%
  arrange(desc(abs(logFC)),desc(p.adj)) %>%
  mutate(up_down = ifelse(logFC>0,"up","down")) %>% 
  filter(up_down=="up") %>% 
  head(n=10) %>%
  pull(Assay)

(violin_malaria_top10 <- data.long %>% 
   inner_join(sampleTable_simple %>% dplyr::select(DAid,Time,sample_id,study_id),
              by="sample_id") %>% 
   dplyr::filter(Assay %in% c(top10up)) %>% 
   mutate(Assay = factor(Assay, levels = top10up)) %>% 
   
   ggplot(aes(x=Time, y=NPX, color=Time,fill=Time)) + 
   geom_line(aes(group=study_id), color="grey",alpha=.6,size=.2)+
   geom_violin(trim = F,alpha=.2,lwd=.25) +
   geom_boxplot(alpha=1,width=0.25,color="black",outlier.size = 0.5, fatten = 1,lwd=.25,show.legend = F) +
   facet_wrap(~Assay,ncol = 5,scales = "free_y") +
   theme_minimal() +
   labs(x="") +
   theme(axis.text.x = element_text(size=6),
         legend.position = "none") +
   scale_color_manual(values=time3_col) +
   scale_fill_manual(values=time3_col))

Figure 1I

top10down <- dap.res %>% dplyr::filter(FDR==TRUE) %>%
  arrange(desc(abs(logFC)),desc(p.adj)) %>%
  mutate(up_down = ifelse(logFC>0,"up","down")) %>% 
  filter(up_down=="down") %>% 
  head(n=10) %>%
  pull(Assay)

(violin_malaria_top10_down <- data.long %>% 
   inner_join(sampleTable_simple %>% dplyr::select(DAid,Time,sample_id,study_id),
              by="sample_id") %>% 
   dplyr::filter(Assay %in% c(top10down)) %>% 
   mutate(Assay = factor(Assay, levels = top10down)) %>% 
    ggplot(aes(x=Time, y=NPX, color=Time,fill=Time)) + 
    geom_line(aes(group=study_id), color="grey",alpha=.6,size=.2)+
    geom_violin(trim = F,alpha=.2,lwd=.25) +
    geom_boxplot(alpha=1,width=0.25,color="black",outlier.size = 0.5, fatten = 1,lwd=.25,show.legend = F) +
    facet_wrap(~Assay,ncol = 5,scales = "free_y") +
    theme_minimal() +
    labs(x="") +
    theme(axis.text.x = element_text(size=6),
          legend.position = "none") +
    scale_color_manual(values=time3_col) +
    scale_fill_manual(values=time3_col))

Supplementary Table S1

##gtsummary
library(gtsummary)
subjectTable %>% 
  mutate(years_since_endemic = case_when(endemic=="primary"~NA,
                                         .default = years_since_endemic),
         
         SOFA_total = as.numeric(SOFA_total),
         endemic = str_replace(endemic,"_"," "),
         severe_5 = case_when(severe_5==1 ~ "severe",.default = "non-severe")) %>% 
  tbl_summary(include = c(sex, age, endemic, years_since_endemic, diff_acuteSample_spt_current.abs, inf_rbc_max, severe_5,SOFA_total),
              
              statistic = list(all_continuous() ~ "{median} ({min}-{max})",
                               all_categorical() ~ "{n} / {N} ({p}%)"
              ),
             # digits = all_continuous() ~ 2,
             digits = c(age ~ 0,
                        years_since_endemic ~ 0,
                        diff_acuteSample_spt_current.abs ~ 0,
                        inf_rbc_max ~ 2),
              label = c(endemic ~ "Previous malaria exposure",
                        age ~ "Age",
                        sex ~"Sex",
                        years_since_endemic ~ "Years since living in endemic area",
                        inf_rbc_max ~ "Parasitemia [%]",
                        SOFA_total ~ "SOFA scale",
                        diff_acuteSample_spt_current.abs ~ "Days since symptom onset",
                        severe_5 = "Severe malaria according to WHO criteria\n(ref WHO Guidelines for the treatment of Malaria , 3rd edition, 2015)"),
              missing = "no"
  ) %>% 
  add_n() %>% # add column with total number of non-missing observations
  modify_header(label = "**Variable**") %>% # update the column header
  bold_labels() 

Variable	N	N = 721
Sex	72
female		17 / 72 (24%)
male		55 / 72 (76%)
Age	72	39 (20-63)
Previous malaria exposure	72
previously exposed		48 / 72 (67%)
primary infected		24 / 72 (33%)
Years since living in endemic area	47	10 (0-33)
Days since symptom onset	69	4 (0-27)
Parasitemia [%]	72	0.80 (0.01-8.00)
Severe malaria according to WHO criteria (ref WHO Guidelines for the treatment of Malaria , 3rd edition, 2015)	72
non-severe		62 / 72 (86%)
severe		10 / 72 (14%)
SOFA scale	72
0		1 / 72 (1.4%)
1		7 / 72 (9.7%)
2		19 / 72 (26%)
3		16 / 72 (22%)
4		13 / 72 (18%)
5		8 / 72 (11%)
6		5 / 72 (6.9%)
9		2 / 72 (2.8%)
12		1 / 72 (1.4%)
1 n / N (%); Median (Minimum-Maximum)

Supplementary Table S2

daps.out <- lme_res_padj %>% 
  transmute(UniProt, 
            Assay,
            estimate,
            contrast, 
            SE,
            CI = 1.96*SE,
            df,
            t.ratio,
            p.value, 
            p.adj,
            preffered_model = case_when(Assay %in% assay_better_complex_model ~ "complex",
                                        .default = "simple"))
#daps.out%>%  write_tsv(paste0(result.dir,"Supplementary_TableS2_DifferentiallyAbundantProteins.tsv"))
daps.out %>% head()

## # A tibble: 6 × 11
##   UniProt Assay    estimate contrast    SE    CI    df t.ratio  p.value    p.adj
##   <chr>   <chr>       <dbl> <chr>    <dbl> <dbl> <dbl>   <dbl>    <dbl>    <dbl>
## 1 P28908  TNFRSF8      2.95 Acute -… 0.194 0.379  66.3    15.2 2.34e-23 3.33e-20
## 2 P22301  IL10         6.62 Acute -… 0.455 0.892  66.3    14.5 2.65e-22 1.38e-19
## 3 Q07325  CXCL9        4.33 Acute -… 0.293 0.574  62.9    14.8 3.86e-22 1.38e-19
## 4 P04233  CD74         2.20 Acute -… 0.134 0.263  52.0    16.4 3.41e-22 1.38e-19
## 5 P20333  TNFRSF1B     2.66 Acute -… 0.185 0.363  66.3    14.4 5.00e-22 1.43e-19
## 6 P19320  VCAM1        1.48 Acute -… 0.105 0.207  66.3    14.0 1.78e-21 4.22e-19
## # ℹ 1 more variable: preffered_model <chr>

Supplementary Figure 1

Figure S1A

tmp <- data.long %>% 
  distinct(sample_id) 
hm_mat <- tmp %>% 
  separate(sample_id, into = c("study_id","Time"),sep = "\\|",remove = T) %>% 
   mutate(Time = factor(Time, levels=c("Acute","D10","M12")),
          dummy = Time) %>% 
  
  group_by(study_id) %>% 
  mutate(n = n()) %>% 
  arrange(-n) %>% 
  ungroup() %>% 
  
  pivot_wider(names_from = Time, values_from = dummy) %>% 
  dplyr::select(-n) %>% 
  column_to_rownames("study_id") %>% 
  relocate(Acute,D10,M12) %>% 
  t() 

(sample_overlap_hm <- hm_mat %>% 
  Heatmap(row_names_gp = gpar(fontsize=6),
          show_column_names = F,
          na_col = "white",
          column_title_gp = gpar(fontsize=6),
          row_names_side = "left",
          column_names_gp = gpar(fontsize=6),
          column_names_rot = 45,
          show_heatmap_legend = F,
          column_split = data.frame(study_id = colnames(hm_mat)) %>% 
            left_join(subjectTable %>% 
                        transmute(study_id, endemic) %>% 
                        bind_rows(
                          tibble(study_id = c("2014003","2012PT12"),
                                 endemic = c("primary_infected","primary_infected")))) %>%  
            transmute(endemic= factor(endemic, levels=c("primary_infected","previously_exposed"), labels= c("primary infected","previously exposed"))),
          row_title_gp = gpar(fontsize=6),
          
          rect_gp = gpar(col = "white", lwd = .5),
          width = ncol(.)*unit(1, "mm"), 
          height = nrow(.)*unit(2, "mm"),
          #height = ncol(.)*unit(1.4, "mm"),
          #  width = ncol(.)*unit(.5,"mm"),
          border_gp = gpar(col = "black", lty = .9),
          col =  time3_col,
          top_annotation = HeatmapAnnotation(df = data.frame(study_id = colnames(.)) %>% 
                                               left_join(subjectTable %>% 
                                                           transmute(study_id, endemic) %>% 
                                                           bind_rows(
                                                             tibble(study_id = c("2014003","2012PT12"),
                                                                    endemic = c("primary_infected","primary_infected"))
                                                             )) %>% 
                                                           dplyr::select(-study_id),
                                                         simple_anno_size = unit(3, "mm"),
                                                         show_annotation_name = F,
                                                         show_legend = F,
                                                         col = list(endemic =  endemic2_col),
                                                         which="column"))
)

Figure S1B

(acute_exposure_volcano <- lme_res %>% 
  unnest(cols=posthoc.time_exposure) %>% 
  filter(contrast %in%c("Acute primary_infected - M12 primary_infected",
                    "Acute previously_exposed - M12 previously_exposed")) %>% 
  ungroup() %>% 
  group_by(contrast) %>% 
  mutate(p.adj = p.adjust(p.value, method="fdr"),
         FDR = ifelse(p.adj <= 0.01, TRUE,FALSE)) %>% 
  arrange(p.adj) %>% 
  transmute(Assay,contrast, estimate,SE,df,t.ratio, p.value, p.adj, FDR,
            color = case_when(FDR==T & contrast=="Acute primary_infected - M12 primary_infected" ~ "primary_infected",
                              FDR==T & contrast=="Acute previously_exposed - M12 previously_exposed" ~ "previously_exposed",
                              .default = NA
                              ),
            contrast = factor(contrast, levels=c("Acute primary_infected - M12 primary_infected",
                                                 "Acute previously_exposed - M12 previously_exposed")),
            label_4_complex_better = case_when(Assay %in% assay_better_complex_model & contrast=="Acute primary_infected - M12 primary_infected" ~ Assay,
                                               .default = NA)) %>% 
  
  ggplot(aes(y=fct_reorder(Assay, estimate), x=estimate, color=color)) +
 
  scale_color_manual(values=endemic2_col, na.value = "grey",breaks = c("primary_infected","previously_exposed")) +
  labs(color=NULL,
       x="Estimated difference +- 95% CI at acute for\nprimary infected and previously exposed individuals\ncompared to M12",#"Estimated difference (NPX) at acute compared to healthy-state at M12",
       y="ranked proteins") +
  geom_errorbar(aes(xmin=estimate - 1.96*SE, 
                    xmax=estimate + 1.96*SE),
                linewidth=.2,    # Thinner lines
                width=.2,
                alpha=.1) +
    geom_point(alpha=0.7,size=.5, shape=16) +
   geom_text_repel(aes(label=label_4_complex_better),#ifelse(Assay %in% assay_better_complex_model & color=="primay_infected",Assay,NA)),
                    show.legend = F,
                   color="black",
                    vjust = .5,
                    hjust = 1,
                    nudge_x = .75,
                    direction = "y",
                    size=1,
                   #label.size = .1,
                    segment.size = 0.2,
                            segment.alpha=.1,
                    max.overlaps = 16) +
  geom_vline(xintercept = 0, lty=2, alpha=.6) +
  theme_minimal())

lme_res_expo <- lme_res %>% 
  unnest(cols="posthoc.time_exposure") %>% 
  filter(contrast=="Acute primary_infected - Acute previously_exposed") %>% 
  ungroup() %>% 
  mutate(p.adj = p.adjust(p.value, method="fdr"),
                  FDR = ifelse(p.adj <= 0.01, TRUE,FALSE)) %>% 
  filter(FDR==T) %>% 
  arrange(-estimate) 

assays_significant_different_at_acute_exp <- lme_res_expo %>% 
  pull(Assay)

Figure S1C

library(eulerr)

plot(euler(list("acute" = lme_res_padj %>% filter(FDR==T) %>% pull(Assay),
                  "exposure"= lme_res_expo %>% filter(FDR==T) %>% pull(Assay))),# assays_significant_different_at_acute_exp)),#lme_res_expo %>% filter(FDR==T) %>% pull(Assay))),
        fills = c("#C51B7D",
                  "white"),
       quantities = TRUE,
       lty = 1,#1:3,
       fontsize=1,
       labels = list(fontsize=5),
       shape = "ellipse",adjust_labels = T)

acut_exposure_intersect <- intersect(assays_significant_different_at_acute_exp,#lme_res_expo %>% filter(FDR==T) %>% pull(Assay),
                                     lme_res_padj %>% filter(FDR==T) %>% pull(Assay))

Figure S1D

df <- lme_res %>% 
  filter(Assay %in% assays_significant_different_at_acute_exp) %>% 
  mutate(Assay = factor(Assay, levels=assays_significant_different_at_acute_exp)) %>% 
  unnest(cols=posthoc.time_exposure) %>% 
  filter(contrast %in%c("Acute primary_infected - M12 primary_infected",
                        "Acute previously_exposed - M12 previously_exposed")) %>% 
  ungroup() %>% 
  mutate(color = case_when(contrast=="Acute primary_infected - M12 primary_infected" ~ "primary_infected",
                           contrast=="Acute previously_exposed - M12 previously_exposed" ~ "previously_exposed",
                              .default = NA
                              )) %>%
 # rownames_to_column("rownumbers") %>% 
  #filter(Assay%in%c("CXCL10","IFNG","CXCL9","TNFSF13B")) %>% 
  dplyr::select(-(lme.res.simple:posthoc.time)) 
require(ggtext)
(acute_exposure_significant <- df %>% 
    mutate(x.label = paste("<span style = 'color: ",
                         ifelse(Assay %in% acut_exposure_intersect , "pink", "black"),
                         ";'>",
                         Assay,
                         "</span>", sep = ""),
         x.label = fct_reorder(x.label, as.character(Assay))) %>%
  ggplot(aes(x=x.label, y=estimate, color=color)) +
  geom_point(shape=16,size=.5) +
  scale_color_manual(values = endemic2_col, breaks = c("primary_infected","previously_exposed")) +

  geom_hline(yintercept = 0, lty=2, alpha=.3) +
 #  ggrepel::geom_text_repel(show.legend = F, color="black") +
  geom_errorbar(aes(ymin=estimate - 1.96*SE, 
                    ymax=estimate + 1.96*SE),
                linewidth=.2,    # Thinner lines
                width=.2,
                alpha=.5) +
  labs(x=NULL,
       color = NULL,
       y="Estimated difference +- 95% CI at acute for\nprimary infected and previously exposed individuals\ncompared to M12\n") +
      theme(axis.text.x = element_markdown(angle = 90, hjust = 1,vjust=0.5, size=6),
            legend.position = "top")
)

Supplementary Figure 2

related to main Figure 2

Figure S2A

supplementary_covariates.res <- data.long %>% 
  inner_join(sampleTable_simple, by="sample_id") %>% 
  inner_join(subjectTable, by="study_id") %>% 
  filter(Time != "D10") %>% 
  mutate(Time = factor(Time, levels=c("Acute","M12"))) %>% 
  group_by(Assay) %>% 
  nest() %>% 
  mutate(lme.res = purrr::map(data, ~ lmerTest::lmer(NPX ~ Time + year_inclusion + sex + age + endemic + inf_rbc_max + (1|study_id), REML = F,
                                           data = .)),
         lme.tidy = purrr::map(lme.res, ~ broom.mixed::tidy(.)))

supplementary_covariates.res_ <- supplementary_covariates.res %>% 
  unnest(cols = lme.tidy) %>% 
  filter(effect =="fixed", 
         term!="(Intercept)") %>% 
  #filter(term != "Residuals") %>% 
  mutate(term = case_when(term=="sexmale"~"sex",
                          term=="endemicprimary_infected"~"endemic",
                          term=="TimeM12"~"Time",
                          .default = term)) %>% 
  mutate(p.adj = p.adjust(p.value, method="fdr")
  ) %>%
  mutate(term.col = case_when(p.adj > 0.01 ~ NA,
                              p.adj <= 0.01 ~ term))

cov.colors <- c("Time" = time3_col[[1]],setNames(brewer.pal(7,"Dark2")[c(1:3,5:8)], c("sex","endemic","age","year_inclusion","inf_rbc_max")))

counts.fdr <- supplementary_covariates.res_ %>% 
  filter(p.adj <= 0.01) %>% 
  group_by(term) %>% 
  count(sort = T)

(data.aov.plot <- supplementary_covariates.res_ %>% 
    mutate(term = factor(term, levels=counts.fdr$term)) %>% 
    ggplot(aes(x=term, y= -log10(p.adj))) + 
    geom_jitter(aes(color=term.col), show.legend = F,size=.25,alpha=.7,shape=16) +
    ggrepel::geom_text_repel(data= . %>% group_by(term) %>% slice_max(n=5,order_by = -log10(p.adj)), 
                             aes(label=Assay), 
                             show.legend = F,force = .5, nudge_y = .25,
                             segment.size=0.2,
                            segment.alpha=.1,
                             size=1,
                             max.overlaps = 15, color="gray45") +
    geom_hline(yintercept=-log10(0.01), 
               linetype = 3) +
    scale_color_manual(values = cov.colors) +
    
    geom_text(data=counts.fdr,aes(x=term, y=-1.2, label=n, color=term), show.legend = F) +
    scale_x_discrete(labels=c("age" = "Age",
                              "year_inclusion" = "Year\nof\nsampling",
                              "sex" = "Sex",
                              "endemic" = "Previous\nexposure",
                              "inf_rbc_max" = "Parasitemia",
                              "Time" = "Infection\n(Acute vs convalescence)")) +
    theme_minimal() +
    labs(x=NULL, 
         color=NULL) +
    theme())

Figure S2B

n2show <- 3
(anova.sex.plot <- supplementary_covariates.res_ %>%
    filter(term=="sex") %>%
    arrange(p.adj) %>% 
    head(n=n2show) %>% 
    unnest(cols = data) %>% 
    ggplot(aes(x=Time, y=NPX, fill=as.character(sex))) +
    geom_boxplot( fatten = 1,lwd=.25,outlier.size = 0.5) +
    facet_wrap(~Assay, scales = "free_y") +
    theme_minimal() +
    labs(x=NULL,
         fill="Sex") +
    scale_fill_manual(values = sex2_col))

(anova.endemic.plot <- supplementary_covariates.res_ %>%
    filter(term=="endemic") %>%
    arrange(p.adj) %>% 
    head(n=n2show) %>% 
    unnest(cols = data) %>% 
    ggplot(aes(x=Time, y=NPX, fill=as.character(endemic))) +
    geom_boxplot(fatten = 1,lwd=.25,outlier.size = 0.5) +
    facet_wrap(~Assay, scales = "free_y") +
    theme_minimal() +
    labs(x=NULL,
         fill="Previous exposure") +
    scale_fill_manual(values = endemic2_col))

(anova.year_inclusion.plot <- supplementary_covariates.res_ %>%
    filter(term=="year_inclusion") %>% arrange(p.adj) %>% 
    head(n=n2show) %>% 
    unnest(cols = data) %>% 
    ggplot(aes(x=as.numeric(year_inclusion),y=NPX,color=Time)) +
    geom_point(size=.5) +
    geom_smooth(linewidth=0.4,
                show.legend = F) +
    scale_x_continuous(limits = c(2011,2021),breaks = c(2011,2016,2021)) + 
    facet_wrap(~Assay, scales = "free_y") +
    theme_minimal() +
    labs(x="Year of inclusion",
      color="Sample time point") +
    scale_color_manual(values = time3_col))

(anova.age.plot <- supplementary_covariates.res_ %>%
    filter(term=="age") %>% arrange(p.adj) %>% 
    head(n=n2show) %>% 
    unnest(cols = data) %>% 
    ggplot(aes(x=as.numeric(age),y=NPX,color=Time)) +
    geom_point(size=.5) +
    geom_smooth(linewidth=0.4,
                show.legend = F) +
    facet_wrap(~Assay, scales = "free_y") +
    theme_minimal() +
    labs(title="",
         x="Years",
         color="Age") + 
    scale_color_manual(values = time3_col)
)

(anova.inf_rbc_max.plot <- supplementary_covariates.res_ %>%
    filter(term=="inf_rbc_max") %>% arrange(p.adj) %>% 
    head(n=n2show) %>% 
    unnest(cols = data) %>% 
    filter(Time=="Acute") %>% 
    ggplot(aes(x=as.numeric(inf_rbc_max),y=NPX,color=as.numeric(inf_rbc_max))) +
    geom_point(size=.5) +
    geom_smooth(aes(color=..x..),
                linewidth=0.4,
                show.legend = F) +
    facet_wrap(~Assay, scales = "free_y") +
    theme_minimal() +
    labs(title="",
         x="Parasitemia, infected erythrocytes [%]",
         color="Parasitemia [%]") + 
    scale_color_gradient(low="grey",high="darkred")
  #scale_color_manual(values = time3_col)
)

(anova.panel <- (anova.inf_rbc_max.plot / 
                   anova.endemic.plot /
                   anova.year_inclusion.plot / 
                   anova.sex.plot/
                   anova.age.plot))

Figure S2C

lme_res.d10 <- data_nested %>% 
  mutate(lme.res = purrr::map(data, ~ lmerTest::lmer(NPX ~ Time + exposure + (1|study_id), REML = F,
                                           control = lme4::lmerControl(check.conv.singular = "ignore"),
                                           data = .x %>% dplyr::filter(Time!="Acute"))),
         #lme.tidy = purrr::map(lme.res, ~ broom.mixed::tidy(.)),
         posthoc.time = purrr::map(lme.res, ~ summary(contrast(emmeans(., ~ Time), method = "pairwise")) %>% tibble())#,
         #posthoc.time_exposure = purrr::map(lme.res, ~ summary(contrast(emmeans(., ~ Time * exposure), method = "pairwise")) %>% tibble())
         )

lme_res.d10_padj <- lme_res.d10 %>% 
  unnest(cols="posthoc.time") %>% 
  filter(contrast=="D10 - M12") %>% 
  #filter(contrast=="Acute primary_infected - Acute previously_exposed") %>% 
  ungroup() %>% 
  mutate(p.adj = p.adjust(p.value, method="fdr"),
         FDR = ifelse(p.adj <= 0.01, TRUE,FALSE)) %>% 
  #   dplyr::rename(logFC = estimate) %>% 
  arrange(p.adj)

acut_d10_list <- list("Acute"=c(lme_res_padj %>% filter(FDR==TRUE, estimate>1) %>% pull(Assay)),
                      "D10" = c(lme_res.d10_padj %>% filter(FDR==TRUE, estimate>1) %>% pull(Assay)))

## venn plot with overlapp numbers
(venn.DAP.acute.d10 <- ggvenn::ggvenn(acut_d10_list,
                                      show_percentage = F,
                                      fill_color = as.character(time3_col[c(1,2)]), 
                                      stroke_size = 0.5,
                                      set_name_size = 2,
                                      text_size = 2,
                                      auto_scale = F,
                                      show_elements = F) +
    theme(plot.title = element_text(hjust = 0.5),
          plot.subtitle = element_text(hjust = 0.5),
          text = element_text(size=6),
          strip.text = element_text(size=6),
          plot.tag = element_text(size=6)))

Figure S2D

(d10_malaria_volcano <-  lme_res.d10_padj %>% 
   arrange(p.adj, abs(estimate)) %>% 
   ggplot(aes(x=estimate, y=-log10(p.adj), color=FDR)) +
   geom_point(alpha=0.7,size=.5, shape=16) +
   ggrepel::geom_text_repel(data = . %>% filter(FDR ==TRUE, abs(estimate) >1),
                            aes(label = Assay), color="black",
                            force        = 0.5,
                            direction    = "both",
                            segment.size = 0.2,
                            segment.alpha=.1,
                            show.legend = F,
                            size=1.5,
                            max.overlaps = 16,
                            box.padding = unit(0.2, "lines"),
                            point.padding = unit(0.5, "lines"),
                            segment.color = 'grey50'
   ) +
   theme_minimal() +
   geom_vline(xintercept = c(-1, 1), linetype = "dotted", size = .5) +
   geom_hline(yintercept = -log10(0.01), linetype = "dotted", size = .5) + 
   scale_x_continuous(breaks=c(-2.5,-1.0,0.0,1.0,2.5,5.0),limits = c(-2.5,5)) +
   labs(x="Estimated difference (NPX)",
        y="-log10(adj. p-value)",
        subtitle= "D10 after disease vs. convalescence",
        caption=paste0("DAP: ",lme_res.d10_padj %>% filter(FDR==TRUE) %>% nrow(),"\n",
                       "DAP up: ",lme_res.d10_padj %>% filter(FDR==TRUE,estimate>0) %>% nrow(),"\n",
                       "DAP FC>1: ",lme_res.d10_padj %>% filter(FDR==TRUE,estimate>1) %>% nrow(),"\n")) +
   theme(legend.position = "none",
         text = element_text(size=6)) +
   scale_color_manual(values= c(time3_col[[3]],time3_col[[2]])))

Figure S2E

(acute_d10_comp <- dap.res %>% 
   ungroup() %>% 
   arrange(-logFC) %>% 
   mutate(row_id=row_number()) %>% 
   mutate(Assay_orders = factor(as.factor(row_id), levels = row_id, labels = Assay),
          Assay_orders = row_id) %>% 
   left_join(lme_res.d10_padj, by=c("Assay","UniProt"),suffix = c(".acute",".d10")) %>% 
   mutate(d = ifelse(estimate>logFC,T,F),
          d_dbl = abs(logFC-estimate)) %>%
   
   ggplot(aes(x=Assay_orders)) +
   geom_segment(data = . %>% filter(p.adj.d10<=0.01, estimate >1), 
                aes(group=Assay, x = Assay_orders, xend = Assay_orders,yend = logFC, y=estimate, color=d), lwd=0.1) +
   geom_point(aes(y=logFC), size=.05, alpha=1, color=time3_col[[1]]) +
   geom_point(data = . %>% filter(p.adj.d10 <=0.05), aes(y=estimate),color=time3_col[[2]], size=.05,alpha=1) +
   
   ggrepel::geom_text_repel(data = . %>% filter(p.adj.d10<=0.05, estimate >1) %>%
                              filter(d==TRUE) %>% 
                              slice_max(order_by = d_dbl,n=10),
                            aes(label = Assay,y=estimate, color=d), 
                            force        = 0.5,
                            direction    = "both",
                            segment.size = 0.1,
                            min.segment.length = 1,
                            nudge_x = 1,
                            show.legend = F,
                            size=2,
                            max.overlaps = 16,
                            box.padding = unit(0.1, "lines"),
                            point.padding = unit(0.5, "lines"),
                            segment.color = 'black') + 
   scale_color_manual(values=c("FALSE" = "navy","TRUE"="red"), labels=c("lower at D10","higher at D10")) +
   geom_hline(yintercept = 0,linetype=3, color=time3_col[[3]]) +
   scale_x_continuous(expand=c(.1,0),
                      trans = "sqrt") + 
   labs(color = NULL,
        x="Proteins ranked by estimated difference (NPX)\nat acute malaria",
        y="Estimated difference (NPX)") +
   theme_minimal() +
   theme(text = element_text(size=6)) 
)

Supplementary Figure 3

related to main Figure 1

Figure S3A

require(clusterProfiler)

length(unique(data$UniProt)) ## 1463

## [1] 1463

entrez_uniprot_name_mapping <- clusterProfiler::bitr(unique(data.long$UniProt), 
                                                     fromType="UNIPROT",
                                                     toType=c("SYMBOL","ENTREZID"),
                                                     OrgDb="org.Hs.eg.db") %>% 
  dplyr::rename(UniProt = UNIPROT,
                Symbol = SYMBOL,
                Entrez = ENTREZID) 

ranks_entrez <- entrez_uniprot_name_mapping %>% 
  inner_join(dap.res %>% ungroup() %>% filter(p.adj<=0.01), by="UniProt") %>%
  arrange(-logFC) %>%
  dplyr::select(Entrez, logFC) %>% deframe()

### KEGG
## all explore proteins
universe.proteins <- data.long %>% distinct(Assay,UniProt) %>% inner_join(entrez_uniprot_name_mapping,by="UniProt")
## prep enrich input
sig_proteins_df <- entrez_uniprot_name_mapping %>% 
  inner_join(dap.res %>% ungroup(), by="UniProt") %>% filter(p.adj <= 0.01) 

# From significant results, we want to filter on log2fold change
sig_proteins <- sig_proteins_df$logFC
# Name the vector
names(sig_proteins) <- sig_proteins_df$Entrez
# omit NA values
sig_proteins <- na.omit(sig_proteins)
# filter on min log2fold change (log2FoldChange > 1)
sig_proteins <- names(sig_proteins)[abs(sig_proteins) > 1]


cp_KEGG.res <- enrichKEGG(
  sig_proteins,
  organism = "hsa",
  #keyType = "UNIPROT",
  pvalueCutoff = 1,
  pAdjustMethod = "BH",
  universe = universe.proteins$Entrez,
  minGSSize = 10, 
  maxGSSize = 500,
  qvalueCutoff = 1,
  use_internal_data = F
)

#data.frame(cp_KEGG.res)


(cp.kegg.acutefc1 <- data.frame(cp_KEGG.res) %>%
    separate(GeneRatio, into=c("hit","total"),sep="/",remove = F,convert=TRUE) %>% 
    head(10) %>% 
    mutate(ratio = hit/total) %>% 
    
    ggplot(aes(x=fct_reorder(Description, -ratio,.desc = TRUE), y=ratio)) +
    geom_bar(stat = "identity", width = 0.05) +
    geom_point(aes(color=-log10(p.adjust))) +#size = 3) +
    geom_text(aes(label=hit),size=2, nudge_y = .01)+
    scale_y_continuous(expand = c(0.02,0), trans = "pseudo_log") +
    scale_x_discrete(expand = c(-0.01, 1)) +
    theme_minimal() +
    theme(text = element_text(size=6 ),
          axis.text.y = element_text(size = 6),
          axis.ticks.x = element_blank()) +
    coord_flip() +
    guides(size = guide_legend(reverse=TRUE)) +
    labs(title = "KEGG_2021_Human",
         x= NULL,
         y = "ratio [protein/total]",
         size="Protein\noverlapp",
         color=expression("-Log"[10]*"(p.adj)"))
  )

Figure S3B

require(pathview)

sig_proteins_df <- entrez_uniprot_name_mapping %>% 
  inner_join(dap.res %>% ungroup(), by="UniProt") %>% filter(p.adj <= 0.01, abs(logFC)>1) 


logFC <- sig_proteins_df$logFC
names(logFC) <- sig_proteins_df$Entrez
pv.out <- pathview(gene.data = logFC, 
                   pathway.id = "hsa04060", 
                   species = "hsa", 
                   limit = list(gene=5, cpd=1),
)

knitr::include_graphics("hsa04060.pathview.png")

KEGG

Figure 2

Potential sources and functionalities of plasma proteins during acute malaria

Figure 2A

secretome_location_dap <- dap.res %>% 
  dplyr::filter(FDR==TRUE) %>%
  arrange(desc(abs(logFC)),desc(p.adj)) %>% 
  inner_join(hpa_24.0, by=c("Assay"="gene","UniProt"="uniprot")) %>% 
  mutate(secretome_location_tissue_spec = case_when(secretome_location=="Not secreted"~ paste0(secretome_location," - ",rna_tissue_specificity),
                                                   .default = secretome_location)) %>% 
  group_by(secretome_location_tissue_spec) %>% 
  count(sort = TRUE) 

## change order
secretome_location_dap.order <- secretome_location_dap %>% pull(secretome_location_tissue_spec)
secretome_location_dap.order <- c("Secreted to blood","Intracellular and membrane","Secreted in other tissues","Secreted to extracellular matrix",
                                  "Secreted to digestive system", "Secreted in brain", "Secreted - unknown location", "Secreted in female reproductive system",
                                  "Secreted in male reproductive system",
                                  "Not secreted - Tissue enriched", "Not secreted - Tissue enhanced","Not secreted - Group enriched", "Not secreted - Low tissue specificity")

## plot everything
(hpa.protein.origin.overview <- secretome_location_dap %>% 
    ungroup() %>% 
    mutate(secretome_location_tissue_spec = factor(as.factor(secretome_location_tissue_spec), levels=rev(secretome_location_dap.order))) %>% 
    ggplot(aes(x=secretome_location_tissue_spec,y=n,fill=secretome_location_tissue_spec)) +
    geom_col(width = 0.5) +
    geom_text(aes(label=n),size=2, nudge_y = -.2) +
    coord_flip() +
    scale_y_continuous(trans="pseudo_log",name = NULL, sec.axis = sec_axis(~.,labels = NULL,breaks = NULL, name = "Number of DAPs"),
                       #expand=c(0,.15)
                       expand=c(0,0)

                       ) +
    theme_bw() +
    theme(axis.text.y = element_text(size = 6),
          axis.text.x = element_text(size = 6),
          legend.text=element_text(size=6),
          legend.title=element_text(size=6),
          plot.title = element_text(size=6))+
    scale_fill_manual(values=secretome_location_tissue_spec_cols,
                      limits = secretome_location_dap.order) +
    labs(fill="Protein\norigin\nby HPA",
         x=NULL))

temp.df <- dap.res %>% 
  dplyr::filter(FDR==TRUE) %>%
  arrange(desc(abs(logFC)),desc(p.adj)) %>% 
  inner_join(hpa_24.0, by=c("Assay"="gene","UniProt"="uniprot")) %>% 
  mutate(secretome_location_tissue_spec = case_when(secretome_location=="Not secreted"~ paste0(secretome_location," - ",rna_tissue_specificity),
                                                   .default = secretome_location))

Figure 2B

df1 <- temp.df %>% 
  transmute(Assay, logFC, p.adj, direction,secretome_location_tissue_spec, secretome_function) 

df2 <- df1 %>% 
  group_by(secretome_location_tissue_spec) %>% 
  summarise(atlas_name_count = n()) %>% 
  left_join(
    df1 %>% 
      group_by(secretome_location_tissue_spec, secretome_function, direction) %>% 
      summarise(function_name_count = n()),
    by="secretome_location_tissue_spec") %>% 
  left_join(
    df1 %>% group_by(secretome_location_tissue_spec, secretome_function, direction) %>% 
      summarise(median_logFC = median(logFC)),
    by=c("secretome_location_tissue_spec", "secretome_function","direction"))

(hpa.function.bubbleplot <- df2 %>% 
    filter(!secretome_location_tissue_spec %in% c("NULL", "NA","no mapping"),
           !secretome_function %in% c("NULL")) %>% 
    mutate(secretome_function = case_when(is.na(secretome_function) ~ "No secretome function",
                                          .default = secretome_function)) %>% 
    mutate(secretome_location_tissue_spec = factor(as.factor(secretome_location_tissue_spec),
                                                  levels=rev(secretome_location_dap.order))) %>% 
    ggplot(aes(x=median_logFC,
               y= fct_reorder2(secretome_function, 
                               atlas_name_count,
                               function_name_count,.desc = F))) +
    geom_point(aes(size=function_name_count, color=secretome_location_tissue_spec), show.legend = T) +
    geom_vline(xintercept = 0,linetype=1) +
    geom_text(aes(label = function_name_count),
              size=2, color="grey20",show.legend = F, parse = F) +
    labs(x="median estimated difference (NPX)",
         y=NULL,
         title = "Number DAPs per HPA function",
         size="Number of proteins",
         caption="Size: number of proteins",
         color = "HPA source") +
    scale_color_manual(values=secretome_location_tissue_spec_cols, limits = secretome_location_dap.order) +
    scale_x_continuous(trans = "pseudo_log") +
    scale_y_discrete(expand = c(0,1))+
    guides(size = "none") +
    theme_minimal() +
    scale_size(range=c(3,6)) +
    theme(text = element_text(size=6))
)

Figure 2C

(acute_malaria_hpa_source <- temp.df %>% 
    right_join(top25 %>% transmute(Assay,logFC)) %>% 
    
    ggplot(aes(x=fct_reorder(Assay,logFC), y=logFC, color=secretome_location_tissue_spec)) +
    geom_point(show.legend = TRUE,size=1) +
    geom_col(width = .05,show.legend = F) +
    scale_y_continuous(sec.axis = sec_axis(~.,labels = NULL,breaks = NULL, name = "Top25 DAP")) +
    coord_flip() +
    theme_minimal() +
    theme(plot.title.position = "plot",
          axis.text.y = element_text(size = 4),
          axis.text.x = element_text(size = 6),
          axis.title.x = element_text(size = 6),
          panel.grid.major = element_blank()) +
    labs(color="HPA source",
         x="",
         y="Estimated difference (NPX)",
         title = "Protein source according to Human Protein Atlas") +
    scale_color_manual(values=secretome_location_tissue_spec_cols,
                       limits=secretome_location_dap.order))

Supplementary Figure 4

related to main Figure 2

Figure S4A

malaria.daps.hpa23 <- dap.res %>% 
  arrange(desc(abs(logFC)),desc(p.adj)) %>% 
  filter(p.adj<=0.01) %>% 
  arrange(-logFC) %>% 
  left_join(hpa_24.0,by=c("UniProt" = "uniprot")) %>% 
  ungroup()

## abundant proteins in acute malaria plasma, not immune cell specific nor predicted to be secreted
## => tissue leakage??
malaria.tissue.leakage <- malaria.daps.hpa23 %>% 
  filter(is.na(rna_blood_cell_specificity) | 
           rna_blood_cell_specificity=="Not detected in immune cells", 
         rna_tissue_specificity %in% c("Tissue enriched"),#,"Group enriched","Tissue enhanced"),
         secretome_location =="Not secreted",
         logFC >0)#.5)

secretome.location.order <- c("Secreted to blood","Intracellular and membrane","Secreted in other tissues","Secreted to extracellular matrix",
                                  "Secreted to digestive system", "Secreted in brain", "Secreted - unknown location", "Secreted in female reproductive system",
                                  "Secreted in male reproductive system","Not secreted")
secretome.fun.count <- malaria.daps.hpa23 %>% group_by(secretome_function) %>% count() %>% arrange(-n) %>% pull(secretome_function)

df <- malaria.daps.hpa23 %>% 
  filter(logFC>=0) %>% 
  transmute(Assay,
            direction,
            secretome_location = factor(secretome_location, levels= secretome.location.order),
            secretome_function = factor(secretome_function, levels = secretome.fun.count),
            rna_blood_cell_specificity,
            rna_tissue_specificity = factor(rna_tissue_specificity, levels = c("Tissue enriched",
                                                                               "Group enriched",
                                                                               "Tissue enhanced",
                                                                               "Low tissue specificity",
                                                                               "Not detected")),
            tissue_enriched = factor(case_when(rna_blood_cell_specificity=="Not detected in immune cells" & rna_tissue_specificity == "Tissue enriched" & secretome_location =="Not secreted" & direction == "up" ~"1",
                                               .default = "0"), 
                                     levels=c("1","0"), 
                                     labels=c("1"="Tissue specific and not secreted",
                                              "0"="Less tissue specific")
            ))

(dap.origin.w.tl <- df %>%
    ggplot(aes(axis1 = secretome_location,
               axis2 = secretome_function,
               axis3 = rna_tissue_specificity,
               axis4 = tissue_enriched
    )) +
    geom_alluvium(aes(fill = secretome_location),width = 1/12,geom = "flow", lode.guidance = "forward",) +
    geom_stratum(aes(fill=secretome_location),width = 1/12) +
    ggfittext::geom_fit_text(stat = "stratum", aes(label = after_stat(stratum)),min.size = 1, show.legend = F) +
    scale_x_discrete(limits = c("Secretome\nlocation","Secretome\nfunction", "Tissue specificity\n(based on gene expression)","Tissue specificity\n(overall)"), expand = c(.2, .05)) +
    theme_bw() +
    scale_fill_manual(values= c(secretome_location_cols,"NA"="red","SPEC"="white")) +
    labs(title = "Abundant proteins in blood during acute malaria",
         y= "Number of proteins") +
    theme(panel.grid.major = element_blank(),
          panel.grid.minor = element_blank(),
          axis.ticks.x = element_blank(),
          panel.background = element_rect(colour = "black", size=0.5, fill=NA),
          panel.border = element_rect(size = 0.2, colour = "grey"),
          legend.position = "none"))

Figure S4B

(alluvial_proteinorigin <- df %>%
   ggplot(aes(axis1 = secretome_location,
              axis3 = rna_tissue_specificity,
              axis4 = tissue_enriched
   )) +
   geom_alluvium(aes(fill = tissue_enriched),width = 1/12,geom = "flow", lode.guidance = "forward",) +
   geom_stratum(aes(fill=secretome_location),width = 1/12) +
   ggfittext::geom_fit_text(stat = "stratum", aes(label = after_stat(stratum)),min.size = 1, show.legend = F) +
   
   scale_x_discrete(limits = c("Secretome\nlocation",#"Secretome\nfunction", 
                               "Tissue specificity\n(based on gene expression)","Tissue specificity\n(overall)"), expand = c(.2, .05)) +
   theme_bw() +
   scale_fill_manual(values= c("Tissue specific and not secreted"="red","Less tissue specific"="grey90")) +
   labs(title = "Potential tissue leakage proteins in blood during acute malaria",
        y= "Number of proteins") +
   theme(panel.grid.major = element_blank(),
         panel.grid.minor = element_blank(),
         axis.ticks.x = element_blank(),
         panel.background = element_rect(colour = "black", size=0.5, fill=NA),
         panel.border = element_rect(size = 0.2, colour = "grey"),
         legend.position = "none"))

malaria.tissue.leakage <- df %>% filter(tissue_enriched=="Tissue specific and not secreted") %>% pull(Assay)

Figure S4C

### tissue expression¨
mat <- hpa.tissue %>% 
  filter(gene_name %in% c(malaria.tissue.leakage)) %>% 
  pivot_wider(names_from = tissue, values_from = n_tpm, values_fn = median) %>% 
  dplyr::select(-gene) %>% 
  column_to_rownames("gene_name")

mat1 <- mat %>% 
  t() %>% 
  scale() %>% 
  scales::rescale(to=c(0,1)) %>% 
  t() 

(hm.tissue.leakage <- mat1 %>% 
    t() %>% 
    Heatmap(row_names_gp = gpar(fontsize=6),
            column_names_gp =  gpar(fontsize=4),
            cluster_rows = T,
            cluster_columns = T,
            name="scaled\nnTPM",
            column_title = "High abundant plasma proteins\n 'Tissue specific and not secreted'",
            column_title_gp = gpar(fontsize=6),
            col = circlize::colorRamp2(c(min(mat1),max(mat1)), c("white","red")),
            column_dend_height = unit(5,"mm"),
            row_dend_width = unit(5,"mm"),
            heatmap_legend_param = list(labels_gp = gpar(fontsize = 6),
                                        title_gp = gpar(fontsize = 6),
                                        legend_height = unit(20, "mm")))
)

Figure S4D

(tissue.leakage.violine <- data.long %>% 
   inner_join(sampleTable_simple %>% dplyr::select(DAid,Time,sample_id,study_id),
              by="sample_id") %>% 
   dplyr::filter(Assay %in% c(malaria.tissue.leakage),#"DEFA1","DEFA1B"),
                 Time!="D10") %>% 
   mutate(Assay = factor(Assay, levels = c(malaria.tissue.leakage))) %>% #,"DEFA1","DEFA1B"))) %>% 
    ggplot(aes(x=Time, y=NPX, color=Time,fill=Time)) + 
    geom_line(aes(group=study_id), color="grey",alpha=.6,size=.2)+
    geom_violin(trim = F,alpha=.2,lwd=.25) +
    geom_boxplot(alpha=1,width=0.25,color="black",outlier.size = 0.5, fatten = 1,lwd=.25,show.legend = F) +
    facet_wrap(~Assay,ncol = 9,scales = "free_y") +
    theme_minimal() +
    labs(x="") +
    theme(axis.text.x = element_blank(),# element_text(size=6),
          legend.position = "bottom") +
    scale_color_manual(values=time3_col) +
    scale_fill_manual(values=time3_col))

Revision extra

df <-  data.long %>% 
   inner_join(sampleTable_simple %>% dplyr::select(DAid,Time,sample_id,study_id),
              by="sample_id") %>% 
  filter(Assay%in% c("AGXT","HAO1"),
         Time=="Acute") %>% 
  left_join(
    clinchem_study_pats_acute.wide %>% transmute(study_id, p_asat, p_alat)
  ) %>% 
  pivot_longer(names_to = "clinchem", values_to = "clinchem_val",cols = p_asat:p_alat)

#cor.test.res <- tidy(cor.test(df$`CD19+ CD20+BAFF-R`,df$TNFSF13B,method = "spearman"))
df %>% 
  transmute(sample_id, Assay,NPX,clinchem,clinchem_val) %>% 
  pivot_wider(names_from = Assay, values_from = NPX) %>%
  pivot_wider(names_from = clinchem, values_from = clinchem_val) %>% 
  column_to_rownames("sample_id") %>% 
  correlation() %>% 
  tibble() %>% 
  filter(Parameter1!=Parameter2,
         Parameter2!="HAO1")

## # A tibble: 5 × 11
##   Parameter1 Parameter2     r    CI CI_low CI_high     t df_error       p Method
##   <chr>      <chr>      <dbl> <dbl>  <dbl>   <dbl> <dbl>    <int>   <dbl> <chr> 
## 1 AGXT       p_asat     0.569  0.95 0.233    0.784  3.39       24 0.00962 Pears…
## 2 AGXT       p_alat     0.410  0.95 0.0994   0.648  2.66       35 0.0273  Pears…
## 3 HAO1       p_asat     0.396  0.95 0.0101   0.679  2.11       24 0.0453  Pears…
## 4 HAO1       p_alat     0.423  0.95 0.115    0.657  2.76       35 0.0273  Pears…
## 5 p_asat     p_alat     0.660  0.95 0.366    0.834  4.30       24 0.00123 Pears…
## # ℹ 1 more variable: n_Obs <int>

df %>% 
  ggplot(aes(x=NPX,y=clinchem_val)) +
  #geom_point(shape=16, size=.5) +
  geom_point() +
  geom_smooth(method="lm") +
  facet_grid(Assay~clinchem)

  #scale_color_manual(values=endemic2_col)+
  #annotate("text",
  #         x=2,
  #         y=7500,
  #         size=1.5,
  #         label=paste("\nrho: ",round(cor.test.res$estimate,2),
  #                     "\np-value:",scales::scientific_format()(cor.test.res$p.value))) +
  #labs(x="TNFSF13B [NPX]\nat Acute",
   #    y="CD19+ CD20+BAFF-R [MFI]\nat Acute",
    #   color=NULL))

library(see)
df %>% 
  transmute(sample_id, Assay,NPX,clinchem,clinchem_val) %>% 
  pivot_wider(names_from = Assay, values_from = NPX) %>%
  pivot_wider(names_from = clinchem, values_from = clinchem_val) %>% 
  column_to_rownames("sample_id") %>% 
  correlation() %>% 
  summary() %>% 
  plot() +

  theme(text = element_text(size=12))

Supplementary Figure 5

related to main Figure 2 ### Figure S5A-D

i="Secreted to blood"
acute_malaria_hpa_function_facet.list <- list()
for(i in c("Secreted to blood","Intracellular and membrane","Secreted in other tissues","Secreted to extracellular matrix","Secreted to digestive system","Secreted in brain","Secreted - unknown location")){
  
  (acute_malaria_hpa_function_facet.list[[i]] <- 
     dap.res %>% 
     dplyr::filter(FDR==TRUE,
                   abs(logFC)>0) %>%
     inner_join(hpa_24.0,by=c("Assay"="gene")) %>% 
     dplyr::filter(secretome_location == i, 
                   !secretome_function %in% c(NA,"NULL","Not secreted")
     ) %>% 
       ungroup() %>% 
       mutate(secretome_function = factor(secretome_function))%>% 
       ggplot(aes(x = fct_reorder2(Assay, secretome_function, -logFC),
                  y=logFC, color = secretome_location)) +
       geom_point(size=1, show.legend = F) + 
       geom_errorbar(aes(ymin= logFC - 1.96*SE,# 1.96*SE =conf.low
                         ymax=logFC + 1.96*SE,#conf.high,
                         color=secretome_location),
                     size=.25,    
                     width=.2,
                     position=position_dodge(.9),
                     alpha=.5) +
       geom_hline(yintercept = 0, linetype=2, alpha=.4) + 
       scale_color_manual(values = secretome_location_cols) +
       coord_flip() +
       theme_minimal() +
       facet_grid(cols = vars(secretome_location), 
                  rows = vars(secretome_function), scales = "free", space = "free_y",drop = F) +
       theme(strip.text.y = element_text(angle = 0,size=3.5),
             strip.placement = "inside",
             axis.text = element_text(size = 3),
             axis.title = element_text(size=5),
             legend.title = element_text(size=5),
             legend.text = element_text(size=5),
             plot.caption = element_text(size=5),
             panel.grid.major.y = element_blank(),
             panel.grid.minor.y = element_blank(),
             panel.grid.major.x = element_line(linewidth = .5),
             panel.grid.minor.x = element_line(linewidth = .5),
             plot.title.position = "plot",
             legend.position = "none") +
       labs(x="",
            y="Estimated difference (NPX) with 95% CI") +
       expand_limits(y = c(-1,1))
  )
}

delta NPX

• needed for heatmap annotation and later on clustering

df_4_fc <- data.wide %>% 
  inner_join(sampleTable_simple %>% dplyr::select(DAid,study_id, sample_id, Time),by="sample_id") %>% 
  dplyr::filter(Time!="D10") %>% 
  dplyr::select(DAid,study_id, sample_id, Time, everything()) %>% 
  pivot_longer(cols = 5:ncol(.), names_to = "Assay", values_to = "NPX") %>% 
  dplyr::select(-DAid,-sample_id) %>% 
  pivot_wider(values_from = "NPX", names_from = "Time")


M12_median_M12 <- df_4_fc %>% 
  group_by(Assay) %>% 
  summarise(m12_median = median(M12,na.rm = TRUE)) 

fc_over_median_M12 <- df_4_fc %>% 
  inner_join(M12_median_M12, by="Assay") %>% 
  group_by(Assay) %>% 
  mutate(log2FC_medianM12 = Acute-m12_median) %>% 
  dplyr::select(-M12) %>% 
  na.omit() %>% 
  dplyr::rename(dNPX = log2FC_medianM12) 

#fc_over_median_M12 %>% saveRDS("../data/data_clean/20230426_Explore1536_fc_over_median_m12_tidy_long.rds")
fc_over_median_M12 %>% head()

## # A tibble: 6 × 5
## # Groups:   Assay [6]
##   study_id Assay   Acute m12_median   dNPX
##   <chr>    <chr>   <dbl>      <dbl>  <dbl>
## 1 2011PT01 NPPB    1.48      0.0487  1.43 
## 2 2011PT01 HNRNPK -0.193     0.658  -0.851
## 3 2011PT01 CEBPB   0.702     0.140   0.562
## 4 2011PT01 CRHR1  -0.829     0.0427 -0.872
## 5 2011PT01 TSLP    0.952     0.154   0.798
## 6 2011PT01 MFAP3   0.871     0.0906  0.781

Figure 3

Single-cell transcriptomics of PBMCs during acute malaria

df <- data.wide %>% 
  inner_join(sampleTable_simple %>% 
               transmute(sample_id),
             by="sample_id") %>% 
  column_to_rownames("sample_id")

## PC calculation
pcaRes <- stats::prcomp(df,center = TRUE, scale. = TRUE)
varExp <- round(pcaRes$sdev^2 / sum(pcaRes$sdev^2) * 100)
pcaDF <- data.frame(PC1 = pcaRes$x[, 1],
                    PC2 = pcaRes$x[, 2]) %>% 
  rownames_to_column("sample_id") 

## Prep for plotting
data4plot <- pcaDF %>% 
  dplyr::inner_join(sampleTable_simple, by="sample_id") %>% 
  mutate(rhapsody_lib = ifelse(study_id == "2013004","Library 1",
                               ifelse(study_id == "2013007","Library 2",
                                      ifelse(study_id == "2013008","Library 3",
                                             ifelse(study_id == "2018002","Library 4",NA)))))


(plot.pca.rhapsody <- data4plot %>% 
    ggplot(mapping = aes(x = PC1, y = PC2, color = Time,fill=NULL, label = NULL)) +
    geom_point(alpha = 0.9, size = 1) +
    ggrepel::geom_text_repel(data= . %>% filter(study_id %in% rhapsody_study_ids), 
                             aes(x=PC1,y=PC2, label=rhapsody_lib),color="grey10",
                             direction = "both",box.padding = 1, max.overlaps = Inf,
                             size=3, alpha=.9,show.legend = F) +
    geom_point(data= . %>% filter(study_id %in% rhapsody_study_ids),
               aes(color=Time),
               size=0.5, alpha=.8) +
    guides(colour = guide_legend(override.aes = list(size=1,alpha=1)))+
    ggplot2::scale_color_manual(values= time3_col) +
    labs(x = paste0("PC1 (",  varExp[1], " %)"),
         y = paste0("PC2 (",  varExp[2], " %)"),
         shape="Rhapsody library") +
    theme_minimal()  +
    theme(legend.title = element_text(size = 6), 
          legend.text = element_text(size = 6))) 

load seurat object & set colors

library(Seurat)
#pbmc <- readRDS("../../MalariaTraveller_AbSeq/data/SeuratObjects/2021-12-17AbSeq_Cell_Calling_qc_cca_wnn_clustering_annotated.rds")
#pbmc <- readRDS("../data/data/rhapsody/2021-12-17AbSeq_Cell_Calling_qc_cca_wnn_clustering_annotated.rds")
pbmc <- readRDS("../data/data/rhapsody/MalariaTraveler_RhapsodyAbSeq_Cell_Calling_qc_cca_wnn_clustering_annotated.rds")

pbmc$Group_rev <- factor(as.factor(pbmc$Group), levels = c("primary", "previously"))

#- RNA Normalization
pbmc <- NormalizeData(object = pbmc, assay = 'RNA', normalization.method = 'LogNormalize', scale.factor = 10000)

#- Ab Normalization
pbmc <- NormalizeData(object = pbmc, assay = 'ADT', normalization.method = 'CLR') #margin   If performing CLR normalization, normalize across features (1) or cells (2)

## list of proteins/mrna targets covered
ab.markers <- rownames(pbmc@assays$ADT)
rna.markers <- rownames(pbmc@assays$RNA)

##change group color
ENDEMIC_colors <- setNames(c("#F1A340","#998EC3"), c("previously_exposed","primary_infected"))
#previously_exposed   primary_infected 
#         "#F1A340"          "#998EC3" 
ENDEMIC_colors <- setNames(brewer.pal(3,"PuOr")[c(1,3)], c("previously_exposed","primary_infected"))
names(ENDEMIC_colors) <- c("previously","primary")
TIME_colors <- setNames(brewer.pal(6,"PiYG"), c("Acute","D10","M1","M3","M6","Y1"))

scaled_01_col <- circlize::colorRamp2(c(0,1), c("white","red"))

L1_colors <- length(unique(pbmc@meta.data$CellType_L1))
L1_colors <- c("#68a748",
               "#8761cc",
               "#ae953e",
               "#688bcc",
               "#cc693d",
               "#4aac8d",
               "#c361aa",
               "#ca5369")
names(L1_colors) <- unique(pbmc@meta.data$CellType_L1)


Idents(pbmc) <- "CellType_L2"

L2_colors <- length(unique(pbmc@meta.data$CellType_L2))
L2_colors <- c("mDC"="#79658C",
               "pDC" = "#AEA14E",
               
               "CD14 monocytes"= "#D1EAB7",
               "CD16 monocytes"="#DB7D47",
               
               "Vd2+ gdT"="#796CD7",
               "Vd2- gdT" =  "#66AC55",
               
               "NK CD56dim CD16+" = "#EBB69E", 
               "NK CD56dim" =  "#CEE486",
               "NK CD56bright"=  "#E0DADB",
               "NK prolif." ="#B5E7DF",
               
               "B naive" = "#889AE5",
               "B memory" = "#66ED58",
               "Plasma cells" = "#893CEA",
               
               "CD4 naive"= "#E15081",
               "CD4 Treg CD80+"= "#579189",
               "CD4 Treg CD80-"=  "#66DEE2",
               "CD4 Tfh"= "#D64EDB",
               "CD4 effect. activated" = "#D38D96",
               "CD4 effect. memory" = "#EDD591",
               "CD4 trans. memory" =  "#DAB8E3",
               "CD4 central memory"  = "#6FE8BE",
               
               "CD8 naive"= "#CAEB48",
               "CD8 trans. memory"= "#85EB8F",
               "CD8 Tfh"="#E6D253",
               "NKT"="#7BBCDF",
               "CD8 effect. memory"  =  "#A7AE90", 
               "undefined"= "#D984D1")

names(L2_colors) <- unique(pbmc@meta.data$CellType_L2)

Figure 3A, C

arr <- list(x = -13, y = -13, x_len = 5, y_len = 5)

umap_axis <- annotate("segment", linewidth=0.1,
                      x = arr$x, xend = arr$x + c(arr$x_len, 0), 
                      y = arr$y, yend = arr$y + c(0, arr$y_len), 
                      arrow = arrow(type = "closed", length = unit(3, 'pt')))
umap_axis_xlab <- annotate("text", x = arr$x+2.5, y = arr$x-1, label = "wnnUMAP 1",size=1) 
umap_axis_ylab <- annotate("text", y = arr$y+2.5, x = arr$y-1, label = "wnnUMAP 2",size=1,angle=90)


rhapsody_umap_coords <- data.table::data.table(pbmc@meta.data, Embeddings(object = pbmc, reduction = 'wnn.umap')) %>% rownames_to_column("CellID") 

lable_df <- rhapsody_umap_coords %>%
  dplyr::group_by(CellType_L1) %>%
  dplyr::select(CellType_L1, contains("UMAP")) %>%
  summarise_all(mean)

(rhapsody_umap_ggplot_l1 <- rhapsody_umap_coords %>% 
    ggplot(aes(x = wnnUMAP_1, y = wnnUMAP_2)) + 
    geom_point(aes(color = as.character(CellType_L1)), size = 0.1, alpha=.5, show.legend = F,shape = 16) +
    ggrepel::geom_text_repel(data=lable_df,aes(x=wnnUMAP_1,y=wnnUMAP_2, label=CellType_L1),size=1.5) +
        coord_fixed()+
    scale_color_manual(values=L1_colors) +
    theme_void() +
                umap_axis +
                umap_axis_xlab +
                umap_axis_ylab)

lable_df <- rhapsody_umap_coords %>%
  dplyr::group_by(CellType_L2) %>%
  dplyr::select(CellType_L2, contains("UMAP")) %>%
  summarise_all(mean)

(rhapsody_umap_ggplot_l2 <- rhapsody_umap_coords %>% 
    ggplot(aes(x = wnnUMAP_1, y = wnnUMAP_2)) + 
    geom_point(aes(color = as.character(CellType_L2)), size = 0.1, alpha=.5, show.legend = F, shape = 16) + 
    ggrepel::geom_text_repel(data=lable_df,aes(x=wnnUMAP_1,y=wnnUMAP_2, label=CellType_L2),size=1.5) +
    labs(x = 'wnnUMAP 1', y = 'wnnUMAP 2', color=NULL)  + 
    coord_fixed()+
    scale_color_manual(values=L2_colors) +
    theme_void() +
                umap_axis +
                umap_axis_xlab +
                umap_axis_ylab)

Figure 3B

require(scales)
(per_sample_perc_l1 <- tibble(pbmc@meta.data) %>% 
    mutate(orig.ident = paste0("Patient"," 0",Library)) %>% 
    group_by(Time,orig.ident) %>% 
    count(CellType_L1) %>% 
    # Stacked + percent
    ggplot(aes(fill = CellType_L1, y=n, x=orig.ident)) + 
    geom_bar(position="fill", stat="identity",width = 0.9) +
    scale_fill_manual(values = L1_colors) +
    facet_grid(~Time,scales = "free_x") +
    scale_y_continuous(labels = scales::percent,expand = c(0,0)) + 
    labs(x = "",
         y = "Frequency",
         fill="") +
    theme_minimal(base_size = 6) +
    #theme_cowplot() +
    theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
          panel.grid.major = element_blank()))

Figure 3D

pbmc_acute <- subset(pbmc, subset=Time=="Acute")

#- RNA Normalization
pbmc_acute <- NormalizeData(object = pbmc_acute, assay = 'RNA', normalization.method = 'LogNormalize', scale.factor = 10000) %>% ScaleData()

#- Ab Normalization
pbmc_acute <- NormalizeData(object = pbmc_acute, assay = 'ADT', normalization.method = 'CLR') #margin   If performing CLR normalization, normalize across features (1) or cells (2)

## Pseudobulk (Celltype)

#https://github.com/satijalab/seurat/discussions/4210
## AverageExpression
Idents(pbmc_acute) <- "CellType_L2"

## calculation of pseudobulk, for each identity based on count data
pbmc_acute.avg.wide <- log1p(Seurat::AverageExpression(pbmc_acute, group.by = "CellType_L2", slot = "counts", verbose = FALSE)$RNA) %>% 
  data.frame() %>% 
  rownames_to_column("gene") 

colnames(pbmc_acute.avg.wide) <- c("gene",colnames(Seurat::AverageExpression(pbmc_acute, group.by = "CellType_L2", slot = "counts", verbose = FALSE)$RNA))

pbmc_acute.avg.long <- pbmc_acute.avg.wide %>% pivot_longer(names_to = "celltype", values_to = "avgExp",cols = -gene)

Mapping (gene - protein)

## mapping 
full_mapping <- mapping_uniprot_ensembl %>% left_join(hpa_24.0, by=c("Ensembl"="ensembl"))

wilcoxUp <- dap.res %>% filter(FDR==TRUE,logFC>1) %>% pull(UniProt)

gene.selection <- full_mapping %>% 
  filter(UniProt %in% wilcoxUp) %>% 
  filter(Symbol %in% rna.markers) %>% distinct(Assay) %>% pull(Assay)

Figure 3D

Heatmap genes expression

rhapsody.gene.match <- full_mapping %>% 
  filter(UniProt %in% wilcoxUp) %>% 
  filter(Symbol %in% unique(pbmc_acute.avg.wide$gene))

## make matrix for heatmap
mat_pbmc_acute <- pbmc_acute.avg.wide %>% 
  filter(gene %in% rhapsody.gene.match$Symbol) %>% 
  column_to_rownames("gene") %>% 
  as.matrix() 

## make row(gene/protein) annotation df
rowAnno.df <- data.frame(Assay = rownames(mat_pbmc_acute)) %>% 
  left_join(dap.res,by=c("Assay")) %>% 
  #left_join(hpa_24.0,by=c("Assay"="gene")) %>% 
    left_join(hpa_24.0,by=c("UniProt"="uniprot")) %>% 

  mutate(secretome_function = ifelse(is.na(secretome_function),"No annotated function", secretome_function))
  

col.anno.df <- data.frame(colnames = colnames(mat_pbmc_acute)) %>% 
  transmute(colnames,
            colanno = case_when(grepl("DC",colnames) ~ "DC",
                                grepl("monocytes",colnames) ~ "Monocytes",
                                grepl("CD4",colnames) ~ "CD4+ T",
                                grepl("CD8",colnames) ~ "CD8+ T",
                                grepl("B|Plasma",colnames) ~ "B",
                                grepl("NK",colnames) ~ "NK",
                                grepl("gdT",colnames) ~ "gdT",
                                .default = "undefined"),
            colanno = factor(colanno, levels= c("DC","Monocytes","NK","gdT","B","CD4+ T","CD8+ T","undefined")))


right.anno <- HeatmapAnnotation(df = col.anno.df %>% column_to_rownames("colnames"), 
                                which = "row",
                                col = list(colanno = L1_colors),
                                # name = "SNF cluster",
                                show_annotation_name = F,
                                show_legend = F,
                                annotation_name_gp = gpar(fontsize=6),
                                annotation_legend_param = list(labels_gp = gpar(fontsize = 6),
                                                               title_gp = gpar(fontsize = 6),
                                                               direction = "horizontal",
                                                               legend_height = unit(.1, "cm"),
                                                               grid_width = unit(.2, "cm")),
                                simple_anno_size = unit(1, "mm"))

top.anno <-  HeatmapAnnotation(df = rowAnno.df %>% transmute(Assay, secretome_location) %>% column_to_rownames("Assay"),
                               which = "column",
                               show_legend = c(TRUE), 
                               show_annotation_name = F, 
                               annotation_name_gp = gpar(fontsize = 6),
                               annotation_legend_param = list(title = "HPA\nclassification",
                                                              title_gp = gpar(fontsize = 6), 
                                                              labels_gp = gpar(fontsize = 6),
                                                              legend_height = unit(3, "mm"), 
                                                              grid_width = unit(3, "mm")),
                               col = list(secretome_location = c(secretome_location_cols)),
                               simple_anno_size = unit(3, "mm"),
                               
                               na_col = "grey90")

## getting foldchange (dNPX over median convalescence) 
m <- fc_over_median_M12 %>%
  filter(Assay %in% rowAnno.df$Assay) %>% 
  pivot_wider(names_from = Assay, values_from = dNPX,id_cols = study_id) %>% 
  column_to_rownames("study_id") %>% 
  as.matrix() %>% t()

m <- m[rownames(mat_pbmc_acute),]


bottom.anno <- HeatmapAnnotation("Plasma protein\ndNPX" = anno_boxplot(t(m),
                                                                       height = unit(1.5, "cm"),width = unit(1.5,"cm"),
                                                                       box_width = 0.8,
                                                                       axis_param = list(side = "right",
                                                                                         labels_rot = 45,
                                                                                         gp=gpar(fontsize = 5)),
                                                                       gp = gpar(fill="#C51B7D"),
                                                                       outline = FALSE),
                                 annotation_name_rot = 0,
                                 annotation_name_gp = gpar(fontsize = 5),
                                 annotation_name_side = "right",
                                 simple_anno_size = unit(3, "mm"),
                                 which = "column")



(pbmc_l2_acute_hm.wide <- mat_pbmc_acute[rownames(m),] %>% 
    t() %>% 
    ## scale values from 0-1
    as.data.frame() %>% mutate(across(where(is.numeric), ~ scales::rescale(., to=c(0,1)))) %>% 
    as.matrix() %>% 
    ComplexHeatmap::Heatmap(
      name="average\ngene\nexpression",
      col = scaled_01_col,
      
      top_annotation = top.anno,
      bottom_annotation = bottom.anno,
      right_annotation =  right.anno,
      column_dend_height = unit(2, "mm"),
      cluster_rows = F,
      row_dend_reorder = TRUE,
      show_row_names = TRUE,
      column_split = rowAnno.df$secretome_function,
      column_dend_reorder = F,
      row_title_side = "right",
      row_title_gp = gpar(fontsize = 6),
      cluster_columns = T,
      row_split = col.anno.df$colanno,
      row_title = NULL,
      
      column_title_gp = gpar(fontsize=4),
      column_title_rot = 45,
      row_title_rot = 0,
      row_names_gp = gpar(fontsize = 4),
      #row_dend_width = unit(2, "mm"), 
      row_dend_side = "left",
      cluster_row_slices = T,
      column_names_gp = gpar(fontsize = 4), 
      column_names_rot = 90,
      heatmap_legend_param = list(labels_gp = gpar(fontsize = 6),
                                  title_gp = gpar(fontsize = 6),
                                  grid_width = unit(3, "mm")),
    ) 
  )

Figure 3E

CellPhoneDB

#cpdb.protein_input <- read_delim("../data/cellphoneDB/v4.1.0_protein_input.csv")
#cpdb.interaction_input <- read_delim("../data/cellphoneDB/v4.1.0_interaction_input.csv")

cpdb.protein_input <- read_delim("../data/cellphoneDB/v5_protein_input.csv",)
cpdb.interaction_input <- read_delim("../data/cellphoneDB/v5_interaction_input.csv")

kegg.ccr <- read_excel("../data/KEGG_CytokineCytokineReceptorInteraction_malariaspec.xlsx") %>% mutate(Source = "KEGG")

rna.markers.uniprot <- data.frame(gene = rna.markers) %>% 
  left_join(hpa_24.0 %>% transmute(gene, uniprot)) %>% na.omit()

ligand.q <- dap.res %>% filter(p.adj <=0.01, logFC > .1) %>% 
  left_join(cpdb.protein_input,
            by=c("UniProt"="uniprot")) %>% 
  pull(UniProt)

length(ligand.q)

## [1] 491

nw <- cpdb.interaction_input %>% 
  filter(partner_a %in% ligand.q,
         directionality == "Ligand-Receptor") %>% 
  mutate(protein_name_b_strip = gsub("_HUMAN","",protein_name_b),
         protein_name_a = gsub("_HUMAN","",protein_name_a)) %>% 
  mutate(protein_name_b_complex = case_when(is.na(protein_name_b) ~ str_remove(interactors,paste0(protein_name_a,"-")),
                                    .default = protein_name_b)) %>%
   separate_longer_delim(protein_name_b_complex, delim = "+") %>% 
   left_join(hpa_24.0 %>% transmute(protein_name_b_complex = gene,
                                      uniprot_b_complex = uniprot), by=c("protein_name_b_complex")) %>% 
  mutate(protein_name_b = case_when(is.na(protein_name_b) ~ protein_name_b_complex,
                                        .default = protein_name_b),
         partner_b_new = case_when(is.na(uniprot_b_complex) ~ partner_b,
                                   .default = uniprot_b_complex)) %>% 
  transmute(partner_a, partner_b, partner_b_new) %>% 
  filter(partner_b_new %in% rna.markers.uniprot$uniprot) %>% 
  mutate(uniprot_a = partner_a,
         uniprot_b = partner_b_new)

measured.in.plasma <- dap.res %>% filter(p.adj <=0.01, logFC > 0.1) %>% pull(UniProt)
measured.in.plasma.name <- dap.res %>% filter(p.adj <=0.01, logFC > .1) %>% pull(Assay)

G <- as_tbl_graph(nw %>% transmute(from = uniprot_a,
                                   to = uniprot_b))
node_table <- as_tibble(G) %>% 
  left_join(dap.res %>% mutate(measured.as.soluble = T),
            by=c("name"="UniProt")) %>% 
  left_join(hpa_24.0 %>% transmute(gene, uniprot), 
            by=c("name"="uniprot")) %>% 
  mutate(protein_name = gene,
         measured.as.soluble = case_when(is.na(measured.as.soluble) ~F,
                                         .default = T))# %>%

(ligand_receptor_nw <- G %>% 
   inner_join(node_table,by="name") %>% 
   create_layout(layout = "fr") %>% 
   ggraph() + 
   geom_edge_link(alpha=.02) + 
   geom_edge_fan(width = .5, color = "grey90") +
   geom_node_point(aes(color=if_else(measured.as.soluble==T,logFC,NA),
                       size= if_else(measured.as.soluble==T,logFC,1))) +
   guides(color = guide_colourbar(barwidth = 3, barheight = .75),
          size=F) +
   labs(color="logFC of proteins\nin plasma") +
   scale_size(range=c(1,3.5)) +
   geom_node_text(aes(label = protein_name,
                      color= if_else(measured.as.soluble==T,logFC,NA)),
                  size=1, 
                  repel=T) +
   scale_color_continuous(low="thistle2",
                          high="darkred", 
                          guide="colorbar",
                          na.value="grey20") +
   theme_void() +
   theme(legend.position = "bottom",
         plot.title = element_text(size=6),
         legend.title = element_text( size=6),
         legend.text=element_text(size=6)) 
)

receptor_fam <- list(cxc_subfam = c("CXCR1","CXCR2","CXCR3","CXCR4","CXCR5","CXCR6","CXCR7","XCR1","CX3CR1"),
                     cc_subfam = paste0("CCR",1:11),
                     class1helicalcyto_fam = c("IL2RA","IL4R"),
                     class2helicalcyto_fam = c("IL10RA","IL10RB"),
                     prolaction_fam = c("GHR","CSF3R"),
                     ifn_fam =c("IFNAR1","IFNAR2","IFNGR1","IFNGR2"),
                     il1likecyto_fam = c("IL1R1","IL1RAP","IL1R2","IL18R1","IL18RAP","ST2","IL1RAP"),
                     nonclassified = c("CD4","CSF1R"),
                     tnf_fam = c("TNFR1","TNFR2","HVEM","FAS","DR4","DR5","DCR1","DCR2","EDAR","RANK","CD27","CD30","CD40","Ox40","TACI"),
                     tgfb_fam = c("TGFBR2","ACVR2B","ACVR1B")) %>% 
  enframe() %>% unnest(cols = c(value)) %>% dplyr::rename(subfam = name, receptor = value)

#extract all transmembrane receptors from CellPhoneDB as uniprotIDs

## filter CellPhoneDB protein_input for transmembrane & receptors
cpdb.receptor.transmem.name <- cpdb.protein_input %>% filter(transmembrane==T |
                                                               receptor==T) %>% 
  mutate(protein_name = gsub("_HUMAN","",protein_name)) %>% 
  pull(uniprot)

df <- pbmc_acute.avg.wide %>% 
  right_join(rna.markers.uniprot) %>% 
  filter(uniprot %in% nw$uniprot_b)

geneAnno <- df %>% transmute(gene,uniprot) %>% left_join(receptor_fam,by=c("gene"="receptor")) %>%
  mutate(subfam = ifelse(is.na(subfam),"Other",subfam),
         CPDB = ifelse(uniprot %in% cpdb.receptor.transmem.name,T,F),
         KEGG = ifelse(gene %in% receptor_fam$receptor,T,F),
         in_plasma = ifelse(gene %in% measured.in.plasma.name,T,F))


mat <- df %>% 
  dplyr::select(-uniprot) %>% 
  column_to_rownames("gene") %>% 
  as.matrix()

col.anno.df <- data.frame(colnames = colnames(mat)) %>% 
  transmute(colnames,
            colanno = case_when(grepl("DC",colnames) ~ "DC",
                                grepl("monocytes",colnames) ~ "Monocytes",
                                grepl("CD4",colnames) ~ "CD4+ T",
                                grepl("CD8",colnames) ~ "CD8+ T",
                                grepl("B|Plasma",colnames) ~ "B",
                                grepl("NK",colnames) ~ "NK",
                                grepl("gdT",colnames) ~ "gdT",
                                .default = "undefined"),
            colanno = factor(colanno, levels= c("DC","Monocytes","NK","gdT","B","CD4+ T","CD8+ T","undefined")))

colAnn.top <- HeatmapAnnotation(df = col.anno.df %>% column_to_rownames("colnames"), 
                                which = "col",
                                col = list(colanno = L1_colors),
                                show_annotation_name = F,
                                show_legend = F,
                                annotation_name_gp = gpar(fontsize=6),
                                annotation_legend_param = list(labels_gp = gpar(fontsize = 6),
                                                               title_gp = gpar(fontsize = 6),
                                                               direction = "horizontal",
                                                               legend_height = unit(.1, "cm"),
                                                               grid_width = unit(.2, "cm")),
                                simple_anno_size = unit(1, "mm")
)

Figure 3F

m <-  mat %>% 
  t() %>% 
  as.data.frame() %>% 
  mutate(across(where(is.numeric), ~ scales::rescale(., to=c(0,1)))) %>% 
  as.matrix() 

(pbmc_l2_acute_cellphonedb_hm.wide <- m %>% 
   ComplexHeatmap::Heatmap(name="average\ngene\nexpression",
                           column_split = geneAnno$subfam, 
                           cluster_columns = T,
                           cluster_column_slices = T,
                           bottom_annotation = HeatmapAnnotation(df=geneAnno %>% transmute(in_plasma),
                                                                 which="column",
                                                                 annotation_legend_param = list(title_gp = gpar(fontsize = 6), 
                                                                                                labels_gp = gpar(fontsize = 6)),
                                                                 annotation_name_gp = gpar(fontsize = 5),
                                                                 simple_anno_size = unit(1.5, "mm"),na_col = c("white","white","white"),
                                                                 show_legend = c(FALSE,FALSE,FALSE),
                                                                 gp = gpar(col = "grey90"),
                                                                 col=list(CPDB = c("TRUE" = "grey60", "FALSE" = "white","NA" = "white"),
                                                                          KEGG = c("TRUE" = "grey60", "FALSE" = "white","NA" = "white"),
                                                                          in_plasma = c("TRUE" = "darkred", "FALSE" = "white","NA" = "white"))),
                           show_row_dend = F,
                           row_title_side = "right",
                           row_title_rot = 0,
                           row_title_gp = gpar(fontsize = 5),
                           row_title = NULL,
                           col = scaled_01_col,
                           row_names_gp = gpar(fontsize = 4),
                           show_column_dend = T,
                           column_dend_height = unit(2,"mm"),
                           row_dend_width = unit(2, "mm"), 
                           row_dend_side = "left",
                           clustering_method_columns = "mcquitty",
                           right_annotation = rowAnnotation(df = col.anno.df %>% column_to_rownames("colnames"), 
                                                            
                                                            col = list(colanno = L1_colors),
                                                            show_annotation_name = F,
                                                            show_legend = F,
                                                            annotation_name_gp = gpar(fontsize=6),
                                                            annotation_legend_param = list(labels_gp = gpar(fontsize = 6),
                                                                                           title_gp = gpar(fontsize = 6),
                                                                                           direction = "horizontal",
                                                                                           legend_height = unit(.1, "cm"),
                                                                                           grid_width = unit(.2, "cm")),
                                                            simple_anno_size = unit(1, "mm")
                           ),
                           cluster_rows = F,
                           row_split = col.anno.df$colanno,
                           column_title_gp = gpar(fontsize=4),
                           column_title_rot = 45,
                           column_names_gp = gpar(fontsize = 4), 
                          heatmap_legend_param = list(labels_gp = gpar(fontsize = 6),
                                  title_gp = gpar(fontsize = 6),
                                  grid_width = unit(3, "mm")))
)

Supplemantary Figure S6

related to main Figure 3

Figure S6A

(rhapsody_cells_per_sample <- tibble(pbmc@meta.data) %>%
  #as.data.table %>% # the resulting md object has one "row" per cell
  rownames_to_column("CellID")  %>% 
  group_by(orig.ident,Time) %>% 
  dplyr::count() %>% 
  ggplot(aes(x=orig.ident,y=n, fill=Time)) +
  scale_fill_manual(values = TIME_colors,breaks = c("Acute","D10","Y1")) +
  scale_y_continuous(expand = c(0,0), trans = "sqrt") +
  coord_flip()+
  geom_bar(stat="identity", position="dodge", show.legend = TRUE) +
  geom_hline(yintercept=6000,lwd=.2) +
  labs(y="Number of cells",
       x="",
       fill="") + 
  theme_minimal())

Figure S6B

## integration
(rhapsody_umap_ggplot_int_orig.ident <- rhapsody_umap_coords %>% 
  ggplot(aes(x = wnnUMAP_1, y = wnnUMAP_2)) + 
  geom_point(aes(color = as.character(orig.ident)), size = 0.1, alpha=.1) +
  labs(x = 'wnnUMAP 1', y = 'wnnUMAP 2', color=NULL)  + 
  guides(color = guide_legend(override.aes = list(alpha = 1,size=.25))) +
  my_dimred_theme
)

Figure S6C

## integration
(rhapsody_umap_ggplot_int_time <- rhapsody_umap_coords %>% 
  ggplot(aes(x = wnnUMAP_1, y = wnnUMAP_2)) + 
  geom_point(aes(color = as.character(Time)), size = 0.25, alpha=.1) +
  labs(x = 'wnnUMAP 1', y = 'wnnUMAP 2', color=NULL)  + 
  scale_color_manual(values = TIME_colors,breaks = c("Acute","D10","Y1")) +
  guides(color = guide_legend(override.aes = list(alpha = 1,size=.25))) +
  my_dimred_theme
)

Figure S6D

(vln_adt.weight <- VlnPlot(pbmc, features = "adt.CCA.weight", group.by = 'CellType_L2', cols = L2_colors, sort = TRUE, pt.size = 0) +
  NoLegend() + 
  labs(title = "adt weight", y="ADT weight",x=NULL))

Figure S6E

rna.marker4dotplot <- c("S100A12","CD14","S100A9","VMO1","C1QA","FCGR3A", "KLRF1","KIR2DL1",
                        "GNLY","IL12RB2","IL18R1","GZMK","TYMS","TOP2A", "KIAA0101","CCR7","LEF1",
                        "MYC", "PASK","CD28","ICOS","RGS1","CTLA4","CCR5","LAG3","POU2AF1",
                        "FOXP3","IL2RA","CD8A","ZNF683","RORC","IKZF2","MS4A1","CD79A","IGKC",
                        "TCL1A","FCER2","CD200","TNFRSF17","FCER1A","CLEC10A","CD1C","NRP1","TLR9","TLR7")

(dotplot.rna <- DotPlot(pbmc,
        features = rna.marker4dotplot,
        assay = "RNA",
        cols = c("RdYlBu"),
        col.min = -2.5,
        col.max = 2.5,
        dot.min = 0,
        dot.scale = 1,
        idents = NULL,
        group.by = NULL,
        split.by = NULL,
        cluster.idents = F,
        scale = TRUE,
        scale.by = "radius",
        scale.min = NA,
        scale.max = NA) + 
  RotatedAxis() + 
  theme(axis.text.x=element_text(size=6), 
        axis.text.y=element_text(size=6),
        text = element_text(size=6)) + 
  labs(x="",y="", title="mRNA expression")
)

DotPlot(pbmc,
        features = rownames(pbmc@assays$ADT),
        assay = "ADT",
        cols = c("RdYlBu"),
        col.min = -2.5,
        col.max = 2.5,
        dot.min = 0,
        dot.scale = 1,
        idents = NULL,
        group.by = NULL,
        split.by = NULL,
        cluster.idents = F,
        scale = TRUE,
        scale.by = "radius",
        scale.min = NA,
        scale.max = NA) + 
  theme(axis.text.x=element_text(size=6), # cell subsets
        axis.text.y=element_text(size=6),
        text = element_text(size=6)) + 
  RotatedAxis() +
  labs(x="",y="", title="Surface protein expression")

Figure S6F

(cellnumbers_l2 <- tibble(pbmc_acute@meta.data) %>% 
   group_by(CellType_L2) %>% 
   count() %>% 
   
   ggplot(aes(fill = CellType_L2, y=n, x=fct_reorder(CellType_L2,n))) + 
   geom_col(show.legend = F) +
   scale_fill_manual(values = L2_colors) +
   scale_y_continuous(expand = c(0, 0),trans  = "log10", breaks=c(1,10,100,1000,5000)) + 
   coord_flip() +
   labs(x=NULL,
        y="Number of cells") +
   theme_bw() +
   theme(panel.grid.major = element_blank(),
         panel.border = element_blank()))

Figure S6G

genes.oi.timepoints = VlnPlot(pbmc,
                              features = c("CD163", "IL1B", "IL1RN", "ICAM1", "LILRB4", "CXCL10", "S100A12",  "NAMPT",
                                           "CCL2", "CXCL11", "CXCL9", "AZU1","VMO1", "TNFRSF8", "CHI3L1","CCL4", "GZMA",
                                           "GZMB","GZMH","CST7","TNFRSF9","IL2RA","IL1RL1","CD48", "CD27", "CD38", "HAVCR2"),
                              group.by = 'CellType_L2', assay = "RNA",
                              split.by = "Time", cols = time3_col, sort = F, pt.size = 0,stack = T,flip = F) +
  theme(axis.text.x = element_text(angle = 0, size=6),
        axis.text.y = element_text(size=6),
        strip.text.x = element_text(angle = 90, size = 5, face=NULL,hjust = .5),
        axis.title.y = element_blank(),
        axis.title.x = element_text(size=6),
        # strip.text.y = element_text(size = 6),
        # strip.text.x = element_text(size=6),
        legend.position = "right",
        legend.key.size = unit(.2, 'cm'), #change legend key size
        legend.key.height = unit(.2, 'cm'), #change legend key height
        legend.key.width = unit(.2, 'cm'), #change legend key width
        legend.title = element_text(size=5), #change legend title font size
        legend.text = element_text(size=5))

genes.oi.timepoints$layers[[1]]$aes_params$size = .1
genes.oi.timepoints

Supplementary Figure 7

related to main Figure 3

dooley <- readRDS("../data/data/ReAnalysis_DooleyNL_etal_bioRxiv_2022/annotated_Sabah_data_21Oct2022.rds")

dooley_colors <- setNames(randomcoloR::distinctColorPalette(length(unique(dooley@meta.data$celltype))),
                          unique(dooley@meta.data$celltype))
## Preliminary QC check

tibble(dooley@meta.data) %>% # the resulting md object has one "row" per cell
  rownames_to_column("CellID")  %>% 
  group_by(orig.ident,timepoint,sample.day,ID) %>% 
  dplyr::count() %>% 
  ungroup() %>% 
  ggplot(aes(x=fct_reorder(orig.ident, timepoint),y=n, fill=ID)) +
  scale_y_continuous(expand = c(0, 0)) +
  coord_flip()+
  geom_bar(stat="identity", position="dodge", show.legend = F) +
  labs(title = "Number of cells per sample",
       x=NULL) +
  theme_minimal()

Figure S7A

dooley_umap_coords <- data.table::data.table(dooley@meta.data, Embeddings(object = dooley, reduction = 'umap')) %>% rownames_to_column("CellID") 

lable_df <- dooley_umap_coords %>%
  dplyr::group_by(celltype) %>%
  dplyr::select(celltype, contains("UMAP")) %>%
  summarise_all(mean)

(dooley_umap_ggplot <- dooley_umap_coords %>% 
    ggplot(aes(x = UMAP_1, y = UMAP_2)) + 
    geom_point(aes(color = as.character(celltype)), size = 0.1, alpha=.5,show.legend = F) +
    ggrepel::geom_text_repel(data=lable_df,aes(x=UMAP_1,y=UMAP_2, label=celltype),size=2) +
    labs(x = 'UMAP 1', y = 'UMAP 2')  + 
    scale_color_manual(values=dooley_colors) +
    my_dimred_theme)

Figure S7B

## Percentage celltype in sample
(dooley_per_sample_perc <- tibble(dooley@meta.data) %>% 
   group_by(timepoint,orig.ident) %>% 
   count(celltype) %>% 
   # Stacked + percent
   ggplot(aes(fill = celltype, y=n, x=orig.ident)) + 
   geom_bar(position="fill", stat="identity",width = 0.9) +
   facet_grid(~timepoint,scales = "free_x",space = "free_x") +
   scale_y_continuous(labels = scales::percent) + 
   scale_fill_manual(values=dooley_colors) +
   scale_y_continuous(labels = scales::percent,expand = c(0,0)) + 
   labs(x = "",
        y = "Frequency",
        fill="") +
   theme_minimal() +
   theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1),
         legend.text = element_text(size=6),
         legend.position = "top",
         panel.grid.major = element_blank()))

get only acute malaria cells (Day0)

dooley_0 <- subset(dooley, subset=timepoint=="Day0")
#- RNA Normalization
dooley_0 <- NormalizeData(object = dooley_0, assay = 'RNA', normalization.method = 'LogNormalize', scale.factor = 10000)

Figure S7C

(dooley_0_cellnumbers <- 
   tibble(dooley_0@meta.data) %>% 
   group_by(celltype) %>% 
   count() %>% 
   ggplot(aes(fill = celltype, y=n, x=fct_reorder(celltype,n))) + 
   geom_col(show.legend = F) +
   scale_y_continuous(expand = c(0, 0),trans  = "log10") +
   coord_flip() +
   scale_fill_manual(values=dooley_colors) +
   labs(x=NULL,
        y="Number of cells") +
   theme_bw() +
   theme(panel.grid.major = element_blank(),
         panel.border = element_blank()))

## calculation of pseudobulk, for each identity based on count data
dooley_0.avg.wide <- log1p(AverageExpression(dooley_0, group.by = "celltype", slot = "counts", verbose = FALSE)$RNA) %>% 
  as.data.frame() %>% 
  rownames_to_column("gene") 

dooley_0.avg.long <- dooley_0.avg.wide %>% 
  pivot_longer(names_to = "celltype", values_to = "avgExp",cols = -gene) %>% filter(avgExp >0)

dooley.gene.match <- full_mapping %>% 
  filter(UniProt %in% wilcoxUp) %>% 
  filter(Symbol %in% unique(dooley_0.avg.long$gene))

mat_dooley_0 <- dooley_0.avg.wide %>% 
  filter(gene %in% dooley.gene.match$Symbol) %>% 
  column_to_rownames("gene") %>% 
  as.matrix() 

Figure S7D

## Rhapsody vs. Dooley
##binning of cell immune cell subsets

#dim(mat_dooley_0)
#dim(mat_pbmc_acute)

## gene overlap Rhapsody, Dooley et al, Explore
rhapsody_dooley_overlapp <- intersect(rownames(mat_dooley_0),rownames(mat_pbmc_acute))

compare_dooley_rhapsody <- data.frame(mat_dooley_0[rhapsody_dooley_overlapp,]) %>% 
  rownames_to_column("gene") %>%
  pivot_longer(cols = -gene) %>%
  mutate(origin = "dooley") %>% 
  bind_rows(
    data.frame(mat_pbmc_acute[rhapsody_dooley_overlapp,]) %>% 
      rownames_to_column("gene") %>% 
      pivot_longer(cols = -gene) %>%
      mutate(origin = "rhapsody")) %>%
  
  
  mutate(name.common = ifelse(grepl("CD14",name),"CD14mono",
                              ifelse(grepl("CD16.monocytes",name,ignore.case = T),"CD16mono",
                                     ifelse(grepl("pDC",name),"pDC",
                                            ifelse(grepl("mDC",name),"mDC",
                                                   ifelse(grepl("NKT",name),"NKT",
                                                          ifelse(grepl("gdT|γδ.T.cells",name),"gdTcell",
                                                                 ifelse(grepl("CD8",name),"CD8T",
                                                                        ifelse(grepl("CD4",name),"CD4T",
                                                                               ifelse(grepl("NK",name),"NK",
                                                                                      ifelse(grepl("B",name),"Bcell",
                                                                                             ifelse(grepl("Unknown|undefined",name),"undefined",
                                                                                                    name)))))))))))) 

common.celltypes <- intersect(filter(compare_dooley_rhapsody,origin=="dooley") %>% pull(name.common),
                              filter(compare_dooley_rhapsody,origin=="rhapsody") %>% pull(name.common))

dooley_hm <- compare_dooley_rhapsody %>% 
  filter(origin=="dooley", name.common %in% common.celltypes) %>% 
  pivot_wider(names_from = gene, values_from = value,id_cols = name.common) %>% 
  column_to_rownames("name.common") %>% 
  ## scale values from 0-1
    as.data.frame() %>% mutate(across(where(is.numeric), ~ scales::rescale(., to=c(0,1)))) %>% 
    as.matrix() %>% 
    t() %>%

  Heatmap(name="Dooley",
          column_title = "Dooley et al.",
          column_title_gp = gpar(fontsize=6),
          
          column_order = common.celltypes,
          col = scaled_01_col,
          cluster_rows = TRUE,
          row_dend_reorder = TRUE,
          show_row_names = TRUE,
          show_heatmap_legend = F,
          row_title_gp = gpar(fontsize = 5),
          row_title_rot = 0,
          row_names_gp = gpar(fontsize = 4),
          row_dend_width = unit(5, "mm"), 
          column_names_gp = gpar(fontsize = 5), 
          column_names_rot = 90,
          heatmap_legend_param = list(labels_gp = gpar(fontsize = 5),
                                      title_gp = gpar(fontsize = 5)),
          width = nrow(.)*unit(.3, "mm"), 
          height = ncol(.)*unit(6, "mm"),
  )

rhapsody_hm <- filter(compare_dooley_rhapsody, origin=="rhapsody", name.common %in% common.celltypes) %>%
  pivot_wider(names_from = gene, values_from = value,id_cols = name.common,values_fn = median) %>% 
  column_to_rownames("name.common") %>% 
  ## scale values from 0-1
    as.data.frame() %>% mutate(across(where(is.numeric), ~ scales::rescale(., to=c(0,1)))) %>% #scale(.))) %>% 
    as.matrix() %>% 
    t() %>%

  Heatmap(name="average\ngene\nexpression",
          column_title = "This study",
          column_title_gp = gpar(fontsize=6),
          column_order = common.celltypes,
          col = scaled_01_col,
          cluster_rows = TRUE,
          row_dend_reorder = TRUE,
          show_row_names = TRUE,
          row_title_gp = gpar(fontsize = 5),
          row_title_rot = 0,
          row_names_gp = gpar(fontsize = 4),
          row_dend_width = unit(5, "mm"), 
          column_names_gp = gpar(fontsize = 5), 
          column_names_rot = 90,
          heatmap_legend_param = list(labels_gp = gpar(fontsize = 5),
                                      title_gp = gpar(fontsize = 5),
                                       title_position = "topcenter"
          ),
          width = nrow(.)*unit(.3, "mm"), 
          height = ncol(.)*unit(6, "mm"),
  )

compare_dooley_rhapsody_hm_new <- dooley_hm + rhapsody_hm

draw(compare_dooley_rhapsody_hm_new, row_dend_side = "left", main_heatmap = "average\ngene\nexpression",auto_adjust = F)

Figure S7E

dim(mat_dooley_0)

## [1] 208  15

row.anno.df <- data.frame(Assay = rownames(mat_dooley_0)) %>% 
  left_join(dap.res,by=c("Assay")) %>% 
  left_join(hpa_24.0,by=c("Assay"="gene")) %>% 
  mutate(secretome_function = ifelse(is.na(secretome_function),"Not secreted", secretome_function)) %>% 
  filter(secretome_function != "Not secreted")

rowAnno <- HeatmapAnnotation(df = row.anno.df %>% transmute(Assay,secretome_location) %>% column_to_rownames("Assay"),
                             which = "row", 
                             show_legend = c(TRUE), 
                             show_annotation_name = F,
                             annotation_name_gp = gpar(fontsize = 5),
                             annotation_legend_param = list(title = "HPA\nclassification",
                                                            title_gp = gpar(fontsize = 5), 
                                                            labels_gp = gpar(fontsize = 5),
                                                            direction="horizontal",
                                                            legend_height = unit(1, "mm"), 
                                                            grid_width = unit(3, "mm"),
                                                            title_position = "topleft"),
                             col = list(secretome_location = secretome_location_cols),
                             simple_anno_size = unit(3, "mm"),
                             na_col = "grey90")

(dooley_day0_hm.hpa.mapping <- mat_dooley_0[row.anno.df$Assay,] %>% 
    t() %>% 
    ## scale values from 0-1
    as.data.frame() %>% mutate(across(where(is.numeric), ~ scales::rescale(., to=c(0,1)))) %>% 
    as.matrix() %>% 
    t() %>% 
    ComplexHeatmap::Heatmap(
      name="average\ngene\nexpression\n",
      col = scaled_01_col,
      right_annotation = rowAnno,
      column_dend_height = unit(2, "mm"), 
      cluster_rows = TRUE,
      row_dend_reorder = TRUE,
      show_row_names = TRUE,
      row_split = row.anno.df$secretome_function,
      row_title_side = "right",
      row_title_gp = gpar(fontsize = 5),
      row_title_rot = 0,
      row_names_gp = gpar(fontsize = 4),
      row_dend_width = unit(4, "mm"), 
      column_names_gp = gpar(fontsize = 5), 
      column_names_rot = 90,
      heatmap_legend_param = list(labels_gp = gpar(fontsize = 5),
                                  title_gp = gpar(fontsize = 5)),
      height = ncol(.)*unit(8, "mm"),
      width = ncol(.)*unit(2,"mm"))
)

Figure S7F

mat_dooley_0 <- dooley_0.avg.wide %>% 
  filter(gene %in% dooley.gene.match$Symbol) %>% 
  column_to_rownames("gene") %>% 
  as.matrix() 

dim(mat_dooley_0)

## [1] 208  15

row.anno.df <- data.frame(Assay = rownames(mat_dooley_0)) %>% 
  left_join(dap.res,by=c("Assay")) %>% 
  left_join(hpa_24.0,by=c("Assay"="gene")) %>% 
  mutate(secretome_function = ifelse(is.na(secretome_function),"Not secreted", secretome_function)) %>% 
  filter(secretome_function == "Not secreted")


(dooley_day0_hm.no.hpa.mapping <- mat_dooley_0[row.anno.df$Assay,] %>% 
    t() %>% 
    ## scale values from 0-1
    as.data.frame() %>% mutate(across(where(is.numeric), ~ scales::rescale(., to=c(0,1)))) %>% #scale(.))) %>% 
    as.matrix() %>% 
    t() %>% 
    ComplexHeatmap::Heatmap(name="average\ngene\nexpression",
                            col = scaled_01_col,
                            show_heatmap_legend = F,
                            column_dend_height = unit(2, "mm"), 
                            cluster_rows = TRUE,
                            row_dend_reorder = TRUE,
                            show_row_names = TRUE,
                            row_split = row.anno.df$secretome_function,
                            row_title_side = "right",
                            row_title_gp = gpar(fontsize = 5),
                            row_title_rot = 0,
                            row_names_gp = gpar(fontsize = 4),
                            row_dend_width = unit(4, "mm"), 
                            column_names_gp = gpar(fontsize = 5), 
                            column_names_rot = 90,
                            heatmap_legend_param = list(labels_gp = gpar(fontsize = 5),
                                                        title_gp = gpar(fontsize = 5)),
                            height = ncol(.)*unit(8, "mm"),
                            width = ncol(.)*unit(2,"mm"))
)

Figure 4

Protein profile-based patient stratification of disease severity

Supplementary Figure 8

** related to main Figure 4**

Figure S8A

clin_marker_cols <- c("CRP","Creatinine","Parasitemia","Platelets","Bilirubin","ASAT","ALAT","Hemoglobin")

clin_marker_cols <- setNames(brewer.pal(length(clin_marker_cols),name="Set3"), clin_marker_cols)



clinical_variables_4circos <-  subjectTable %>% 
    left_join(clinchem_study_pats_acute.wide, by="study_id") %>% 
    #inner_join(patient_clust,by="study_id") %>% 
    ungroup() %>% 
    pivot_longer(cols = c(plt_count_min,inf_rbc_max,crp_max,hb_min,bili_max,crea_max,"p_alat","p_asat"),
                 names_to = "clin.var", values_to="clin.val",
    ) %>% 
    drop_na(clin.val) %>% 
    group_by(clin.var) %>% 
 mutate(n_group= as.character(n()),
           label_group= factor(paste0('\n n = ', n_group))) %>% 
    mutate(clin.var = case_when(clin.var=="crp_max"~"CRP",
                          clin.var=="p_alat"~"ALAT",
                          clin.var=="p_asat"~"ASAT",
                          clin.var=="plt_count_min"~"Platelets",
                          clin.var=="inf_rbc_max" ~"Parasitemia",
                          clin.var=="bili_max"~"Bilirubin",
                          clin.var=="hb_min" ~"Hemoglobin",
                          clin.var=="crea_max"~"Creatinine",
                          .default=clin.var)) %>% 
    mutate(clin.var = factor(clin.var, levels=names(clin_marker_cols))) 
 
(clin_para_whole_cohort <- clinical_variables_4circos %>% 
    ggplot(aes(x=label_group, y=clin.val, fill=clin.var)) +
    geom_violin(trim=F, show.legend = F, width=.4,lwd=.25) +
    geom_jitter(size=0.05,width = .1, show.legend = F,lwd=.25) +
    geom_boxplot(alpha=.7, outlier.shape = NA, width=.2, show.legend = F,lwd=.25) +
    facet_wrap(~clin.var, scales = "free", nrow = 4,
    labeller = labeller(clin.var = c("Bilirubin"= "Bilirubin\n(\U003BCmol/L)",
                                     "ALAT"="ALT\n(U/L)",
                                     "ASAT"="AST\n(U/L)",
                                     "CRP"="CRP\n(mg/L)",
                                     "Parasitemia"="Parasitemia\n(%)", 
                                     "Creatinine"="Creatinine\n(\U003BCmol/L)",
                                     "Hemoglobin"="Hemoglobin\n(g/dL)",
                                     "Platelets"="Platelet\n(counts)"))) +
    theme_bw(base_size = 6)+
    labs(y="Clinical parameter value",
         x=NULL) +
  scale_fill_manual(values=clin_marker_cols))

Figure S8C

patient_SOFA <- subjectTable %>% dplyr::select(study_id, contains("SOFA"))

who22_severemalaria <- subjectTable %>% 
  transmute(study_id,
            respiratory_distress = case_when(pulm_edema == 1 |
                                               resp_distress == 1 |
                                               ards == 1 ~ 1, 
                                             .default = 0),
            circ_80,
            hb_70 = case_when(hb_min <= 70 ~ 1, 
                              hb_min >70 ~0,
                              .default = NA),
            bili_50,
            crea_265 = case_when(crea_max >= 265 ~ 1, 
                                 crea_max <265 ~ 0,
                                 .default = NA),
            parasitaemia_2 = case_when(inf_rbc_max >= 2 ~ 1,
                                       inf_rbc_max < 2 ~ 0,
                                       .default = NA),
            parasitaemia_5 = case_when(inf_rbc_max >= 5 ~ 1,
                                       inf_rbc_max < 5 ~ 0,
                                       .default = NA)
  )

mat <- who22_severemalaria %>% 
  column_to_rownames("study_id") %>% 
  as.matrix() %>% 
  t()

mat_sofa_total <- data.frame(study_id = colnames(mat)) %>% 
  left_join(patient_SOFA, by="study_id") 

study_id_SOFA.sorted <- mat_sofa_total %>% arrange(-SOFA_total) %>% pull(study_id)

mat <- mat[,study_id_SOFA.sorted]


severesign_count <- who22_severemalaria %>% 
  transmute(study_id,
            respiratory_distress,
            circ_80,
            hb_70,
            bili_50,
            crea_265,
            parasitaemia_5) %>% 
  replace(is.na(.), 0) %>% 
  rowwise() %>%
  mutate(nr_of_severe_signs = sum(c_across(where(is.numeric)))) %>% 
  transmute(study_id,
            nr_of_severe_signs) 

(hm.sofa.clin <- mat %>% 
  Heatmap(name = "Severe malaria symptoms\ndefined by WHO 2015",
          col = c("0"="white","1"="#C51B7D"),
          column_names_gp = gpar(fontsize = 6), 
          na_col = "grey90",
          cluster_columns = F,
          cluster_rows = F,
          show_row_dend = F, 
          show_column_dend = F,
          show_column_names = F,
          top_annotation = HeatmapAnnotation(df = data.frame(study_id = colnames(mat)) %>%
                                               left_join(severesign_count) %>%
                                               column_to_rownames("study_id"),
                                             gp = gpar(fontsize=6),
                                             annotation_legend_param = list(labels_gp = gpar(fontsize = 6),
                                                                            title_gp = gpar(fontsize = 6),
                                                                            direction = "horizontal",
                                                                            title_position = "topcenter",
                                                                            title = "Nr of\nsevere malaria\nsymptoms"),
                                             simple_anno_size = unit(2, "mm"),
                                             annotation_name_gp = gpar(fontsize=6),
                                             col = list(nr_of_severe_signs = circlize::colorRamp2(c(0,6), c("white","orange")))),
          row_title_side = "left",
          row_title_rot = 0,
          row_title_gp = gpar(fontsize = 6),
          column_title_side = "top",
          row_names_gp = gpar(fontsize = 6),
          row_dend_width = unit(0.5, "cm"), 
          column_title_gp = gpar(fontsize = 6),
          column_names_rot = 90,
          heatmap_legend_param = list(labels_gp = gpar(fontsize = 6),
                                      title_gp = gpar(fontsize = 6), 
                                      title_position = "topcenter",
                                      at = c(0,1),
                                      labels = c("no","yes")),
          bottom_annotation = HeatmapAnnotation(df = data.frame(study_id = colnames(mat)) %>% 
                                left_join(patient_SOFA, by="study_id") %>% 
                                dplyr::select(-study_id) %>% 
                                as.data.frame(),
                              which = 'col', 
                              gp = gpar(fontsize=6),
                              simple_anno_size = unit(2, "mm"),
                              annotation_name_gp = gpar(fontsize=6),
                              col = list(SOFA_total = colorRamp2(c(min(patient_SOFA$SOFA_total,na.rm = TRUE),
                                                                   median(patient_SOFA$SOFA_total,na.rm = TRUE),
                                                                   max(patient_SOFA$SOFA_total,na.rm = TRUE)),
                                                                 c(brewer.pal(3,name="PuBu"))),
                                         SOFA_liver = SOFA_sub_col,
                                         SOFA_cns = SOFA_sub_col,
                                         SOFA_coag = SOFA_sub_col,
                                         SOFA_resp = SOFA_sub_col,
                                         SOFA_cardio = SOFA_sub_col,
                                         SOFA_renal = SOFA_sub_col),
                              show_legend = c(T,F,F,F,F,F), 
                              annotation_legend_param = list(SOFA_total = list(title = "SOFA (total)",
                                                                               labels_gp = gpar(fontsize = 6),
                                                                               title_gp = gpar(fontsize = 6),
                                                                               direction = "horizontal",
                                                                               title_position = "topcenter"
                                                                               ),
                                                             SOFA_cns = list(title="SOFA (subcategorical)",
                                                                             labels_gp = gpar(fontsize = 6),
                                                                             title_gp = gpar(fontsize = 6),
                                                                             direction = "horizontal",
                                                                             title_position = "topcenter"))),
          width = ncol(.)*unit(1.3, "mm"), 
          height = nrow(.)*unit(1.6, "mm"),
          rect_gp = gpar(col = "grey80", lwd = .2),
          border_gp = gpar(col = "black", lty = .5)))

Figure S8D-E

data4_pcaRes_FCmedian <- fc_over_median_M12 %>% 
  filter(Assay %in% c(dap.res %>% filter(FDR==TRUE, abs(logFC)>1) %>% pull(Assay))) %>% 
  pivot_wider(values_from = dNPX, names_from = Assay, id_cols = study_id) %>% column_to_rownames("study_id") 

## PC calculation
pcaRes_FCmedian <- prcomp(data4_pcaRes_FCmedian, center = TRUE, scale. = TRUE)

varExp_FCmedian <- round(pcaRes_FCmedian$sdev^2 / sum(pcaRes_FCmedian$sdev^2) * 100)

#sum(varExp_FCmedian[1:6])

pcaDF_FCmedian <- data.frame(pcaRes_FCmedian$x) %>% 
  rownames_to_column("study_id") %>% dplyr::select(1:10) %>% 
  inner_join(data4_pcaRes_FCmedian %>% rownames_to_column("study_id"), by="study_id")

(pca_FCmedian <- pcaDF_FCmedian %>% 
    ggplot(aes(x=PC1,y=PC2)) +
    geom_point(size=.5) + 
    my_dimred_theme +
    coord_fixed(ratio = 1.75) +
    labs(x=paste0("PC1 (",varExp_FCmedian[1],"%)"),
         y=paste0("PC2 (",varExp_FCmedian[2],"%)"),
         title = "dNPX (delta NPX of acute over convalescence median)",
         caption = paste0("# samples: ",dim(data4_pcaRes_FCmedian)[1],
                          "\n # proteins: ",dim(data4_pcaRes_FCmedian)[2],
                          "\nlogFC>1")
    ))

(acute.dnpx.ellbow <- data.frame(PC = 1:10,
           varExp = varExp_FCmedian[1:10]) %>% 
  ggplot(aes(x=PC, y=varExp)) +
  scale_y_continuous(breaks = seq(0, 35, by = 5)) +
  geom_point(size=.2) +
  geom_line(lwd=.2) +
  theme_minimal() +
  scale_x_continuous(limits=c(1,10), breaks = c(1:10)))

df <- pcaDF_FCmedian %>% 
  dplyr::select(study_id,PC1:PC6) %>% 
  column_to_rownames("study_id") 

set.seed(2023L)
km <- kmeans(df, centers = 3, nstart = 25) 

km.res <- data.frame(study_id = rownames(df)) %>% inner_join(data.frame(cluster = km$cluster) %>% rownames_to_column("study_id"), by="study_id") 

patient_clust <- km.res %>%
  inner_join(subjectTable %>% transmute(study_id, SOFA_total),by="study_id") %>% 
  group_by(cluster) %>% 
  summarise(meanSOFA_total = mean(SOFA_total)) %>% 
  arrange(-meanSOFA_total) %>% 
  mutate(severity_lab = c("severe","moderate","mild")) %>% 
  rownames_to_column("rowname") %>% 
  mutate(rowname = as.numeric(rowname)) %>% 
  left_join(km.res %>% transmute(study_id,cluster)) %>% 
  mutate(cluster.orig =  fct_reorder(as.factor(cluster),rowname),
         severity_lab = fct_reorder(as.factor(severity_lab),rowname),
         cluster = fct_reorder(as.factor(rowname),rowname))

patient_clust %>% write_tsv(file = paste0(result.dir,"PatientClustering.tsv"))
patient_clust %>% saveRDS(file = paste0(result.dir,"PatientClustering.rds"))

Figure S8D-F

pca_FCmedian

acute.dnpx.ellbow

(pcaDF_FCmedian_PC1_6_hm <- pcaDF_FCmedian %>% 
  dplyr::select(study_id,PC1:PC6) %>% 
  column_to_rownames("study_id") %>% 
  t() %>% 
  Heatmap(name="PC value",
          column_km = 3,
          show_column_names = F,
          row_names_gp = gpar(fontsize=6),
          row_dend_width = unit(3, "mm"), 
          column_dend_height = unit(6,"mm"),
          column_title_gp = gpar(fontsize = 6), 
          heatmap_legend_param = list(labels_gp = gpar(fontsize = 6),
                                      title_gp = gpar(fontsize = 6),
                                      legend_height = unit(1, "mm"), 
                                      title_position = "topcenter"))
)

Figure S8G

df_acute_patclust_incl_conv <- data.long %>% 
  inner_join(sampleTable_simple %>% dplyr::select(DAid,Time,sample_id,study_id),by="sample_id") %>% 
  inner_join(patient_clust,by="study_id") %>% 
  
  filter(Time=="Acute") %>% 
  ## adding data for M12 time point
  bind_rows(data.long %>% 
              inner_join(sampleTable_simple %>% dplyr::select(DAid,Time,sample_id,study_id),by="sample_id") %>% 
              inner_join(patient_clust,by="study_id") %>% 
              filter(Time=="M12") %>% 
              mutate(severity_lab = "convalescence")) %>% 
  mutate(severity_lab = factor(as.factor(severity_lab),
                               levels=c("severe","moderate","mild","convalescence"),
                               labels=c("severe","moderate","mild","convalescence"))) 

my_comparisons_severe_conv <- list(c("severe", "moderate"), c("moderate", "mild"), c("severe", "mild"),c("mild","convalescence"))

(liver.tissueleakage.severity.plot <- df_acute_patclust_incl_conv %>%
  filter(Assay %in% c("AGXT","HAO1")) %>% 
  ggplot(aes(x=severity_lab, y=NPX, color=severity_lab, fill=severity_lab)) + 
  geom_violin(trim = F,alpha=.9) +
  geom_jitter(size=0.25,show.legend = F, width = 0.05, alpha=1, color="grey20") +
  geom_boxplot(alpha=.7,width=0.25,outlier.shape = NA,color="black", fatten = 2,lwd=.25,show.legend = F) +
  stat_compare_means(method = "wilcox.test",
                     label.sep = "\n",
                     hide.ns = T,
                     label = "p.signif" ,
                     vjust = .5,
                     size=2,
                     lwd = .2,
                     comparisons =my_comparisons_severe_conv,
                     show.legend = F) +
  facet_wrap(~Assay,ncol = 8,scales = "free_y") +
  theme_minimal() +
  theme(legend.position="bottom",
        axis.text.x = element_blank()) +
  labs(x="",
       color=NULL,
       fill=NULL) +
  scale_color_manual(values= c(patient_kclust3_lab_conv)) + 
    scale_fill_manual(values= c(patient_kclust3_lab_conv))
)

Figure 4A

(acute.dnpx.pca.clustered <- pcaDF_FCmedian %>% 
  inner_join(patient_clust) %>% 
  ggplot(aes(x=PC1,y=PC2, color=cluster)) +
  geom_point(size=.5) +
    scale_color_manual(values=patient_kclust3) +

  labs(color="Cluster",
       title="dNPX") +
  coord_equal(ratio = 1.5)  + theme_minimal())

acute.dnpx.pca.clustered


 ggExtra::ggMarginal(acute.dnpx.pca.clustered, type="density",groupColour = TRUE, groupFill = TRUE)

Figure 4B

my_comparisons <- list(c("1", "2"), c("2", "3"), c("1", "3"))

(clusters_sofa <- subjectTable %>% 
    inner_join(patient_clust,by="study_id") %>% 
    
    ggplot(aes(x=cluster, y=SOFA_total, color=cluster, fill=cluster)) +
    geom_jitter(width = 0.2,show.legend = T, size=0.5,alpha=.7) +
    geom_boxplot(alpha=1,width=0.3,color="black",outlier.colour = NA, fatten = 2,lwd=.25,show.legend = F) +
    labs(title = paste0("Sequential Organ Failure Assessment (SOFA) score")) + 
    scale_color_manual(values=patient_kclust3)+
    scale_fill_manual(values=patient_kclust3) +
    scale_y_continuous(limits = c(0,16)) +
    stat_compare_means(method = "wilcox.test",
                       label.sep = "\n",
                       hide.ns = T,
                       label = "p.signif" ,
                       vjust = .5,
                       size=2,
                       lwd = .2,
                       comparisons =my_comparisons) +
    theme_minimal()+
    theme(legend.position ="none"))

Figure 4C

prot.data.4.corr <- data.long %>%
  inner_join(dap.res,by=c("Assay", "UniProt")) %>% 
  filter(p.adj<=0.05,
         abs(logFC)>1,
  ) %>% 
  pivot_wider(values_from = NPX, names_from = Assay,id_cols = sample_id) %>% 
  inner_join(sampleTable_simple %>% filter(Time=="Acute") %>% transmute(sample_id,study_id), by="sample_id") %>%
  dplyr::select(-sample_id) %>% 
  dplyr::select(study_id, everything()) 


clinical.feat.list <- c("inf_rbc_max", "resp_rate_max","sat", "syst_bp_min",
                        "p_alat", "p_asat",
                        "hb_min","wbc_count","plt_count_min","crp_max","bili_max","crea_max","SOFA_cns","SOFA_liver","SOFA_renal","SOFA_coag","SOFA_resp","SOFA_total")
  
clin.data.4.corr <-
  subjectTable %>% 
      left_join(clinchem_study_pats_acute.wide, by="study_id") %>% 

  dplyr::select(study_id, all_of(clinical.feat.list))


my_comparisons_severe <- list(c("severe", "moderate"), c("moderate", "mild"), c("severe", "mild"))

df <- clin.data.4.corr %>% 
  dplyr::select(study_id, clinical.feat.list, -contains("SOFA")) %>% 
  pivot_longer(cols= -study_id) %>% 
  inner_join(patient_clust) %>% 
  na.omit() %>% 
  group_by(name, severity_lab) %>% 
  mutate(n_group= as.character(n()),
                  label_group= factor(paste0('n = ', n_group))) %>% 
    ungroup() %>% 
  group_by(name) %>% 
   mutate(label_pos = min(value),
          subcat = case_when(name %in% c("bili_max", "p_alat","p_asat") ~ "Liver function",
                             name %in% c("hb_min","wbc_count", "plt_count") ~ "Blood cells",
                             name %in% c("resp_rate_max","sat","syst_bp_min") ~ "Circulation",
                             .default=NA)) %>% 
   ungroup() %>% 
  mutate(name = factor(name, levels = c("crp_max","crea_max","inf_rbc_max",
                                         "hb_min","wbc_count","plt_count_min",
                                         "bili_max","p_asat","p_alat",
                                         "resp_rate_max","sat","syst_bp_min"
                                         ))) 

single_facet_fun = function(data)( 
  data %>% 
    ggplot(aes(x=severity_lab, y=value, fill= severity_lab)) +
    geom_violin(trim=F, show.legend = F, width=.6,lwd=.25) +
    geom_jitter(size=0.05,width = .1, show.legend = F) +
    geom_boxplot(aes(fill=severity_lab),alpha=.7, outlier.shape = NA,width=.2, show.legend = F,lwd=.25) +
    theme_bw(base_size = 6) +
    scale_y_continuous(expand=c(.2,0))+
    facet_grid(~label_name) +
    theme(axis.title.x = element_blank()) +
    scale_fill_manual(values=patient_kclust3_lab) +
    stat_compare_means(method = "wilcox.test",
                       label.sep = "\n",
                       hide.ns = T,
                       label = "p.signif", 
                       vjust = 0.5,
                       size=2,
                       comparisons = my_comparisons_severe) +
    labs(fill=NULL,
         x=NULL) +
    scale_x_discrete(labels=data$label_group))


## 
p_list <- df %>% 
  mutate(name = factor(name, levels = c("crp_max","crea_max","inf_rbc_max",
                                         "hb_min","wbc_count","plt_count_min",
                                         "bili_max","p_asat","p_alat",
                                         "resp_rate_max","sat","syst_bp_min"
                                         )),
         label_name = case_when(name == "bili_max" ~ "Bilirubin\n(\U003BCmol/L)",
                                name == "crea_max" ~ "Creatinine\n(\U003BCmol/L)",
                                name == "crp_max" ~ "CRP\n(mg/L)",
                                name == "hb_min" ~ "Hemoglobin\n(g/L)",
                                name == "inf_rbc_max" ~ "Parasitemia\n(%)",
                                name == "plt_count_min" ~ "Platelet\n(counts)",
                                name == "sat" ~ "Saturation\n(%)",
                                name == "p_asat" ~ "AST\n(U/L)",
                                name == "p_alat" ~ "ALT\n(U/L)",
                                name == "resp_rate_max" ~ "Respirations rate\n(bpm)",
                                name == "wbc_count" ~ "White blood cells\n(counts)",
                                name == "syst_bp_min" ~ "Systolic blood\npressure (mmHg)"
               ),
         label_unit = case_when(name == "bili_max" ~ "unit",
                                name == "crea_max" ~ "unit",
                                name == "crp_max" ~ "mg/L",
                                name == "hb_min" ~ "g/dL",
                                name == "inf_rbc_max" ~ "%",
                                name == "plt_count_min" ~ "counts",
                                name == "sat" ~ "%",
                                name == "p_asat" ~ "unit",
                                name == "p_alat" ~ "unit",
                                name == "resp_rate_max" ~ "bpm",
                                name == "wbc_count" ~ "counts",
                                name == "syst_bp_min" ~ "mmHg"
               )) %>% 
  arrange(name) %>% 
  group_by(name) %>% 
  nest() %>% 
  mutate(single_plot = purrr::map(data, single_facet_fun))
         

clin.data.severity.groups.new <- wrap_plots(p_list$single_plot, ncol=3)

clin.data.severity.groups.new.data <- p_list %>%
  unnest(data) %>% 
  compare_means(
    value ~ severity_lab, data = ., group.by = "name",
    method = "wilcox.test") %>% 
  transmute(name, group1, group2, p, p.adj, p.signif, method) 

## show plot
clin.data.severity.groups.new

Figure 4D

## nest data
#data_nested <- data.long %>% 
#  inner_join(sampleTable_simple, by="sample_id") %>% 
#  left_join(subjectTable %>% transmute(study_id, 
#                                       exposure = factor(endemic, levels=c("primary_infected","previously_exposed"))),
#            by="study_id") %>% 
#  group_by(UniProt,Assay) %>% 
#  nest()

#lme_res <- data_nested %>% 
#  mutate(lme.res = purrr::map(data, ~ lmer(NPX ~ Time * exposure + (1|study_id), REML = F,
#                                           data = .x %>% dplyr::filter(Time!="D10"))),
#         lme.tidy = purrr::map(lme.res, ~ broom.mixed::tidy(.)),
#         posthoc.time = purrr::map(lme.res, ~ summary(contrast(emmeans(., ~ Time), method = "pairwise")) %>% tibble()),
#         posthoc.time_exposure = purrr::map(lme.res, ~ summary(contrast(emmeans(., ~ Time * exposure), method = "pairwise")) %>% tibble())
#         )

######
data_nested.patclust <- data.long %>% 
  inner_join(sampleTable_simple, by="sample_id") %>% 
  inner_join(patient_clust,by="study_id") %>% 
  mutate(all_vs_1 = ifelse(cluster.orig %in% c("2","3"),"rest",
                           ifelse(cluster.orig =="1","1",NA)),
         all_vs_2 = ifelse(cluster.orig %in% c("1","3"),"rest",
                           ifelse(cluster.orig =="2","2",NA)),
         all_vs_3 = ifelse(cluster.orig %in% c("2","1"),"rest",
                           ifelse(cluster.orig =="3","3",NA))) %>% 
  group_by(UniProt,Assay) %>% 
  nest()

g_vs_conv <- data_nested.patclust %>%
   mutate(lme.res = purrr::map(data, ~ lmer(NPX ~ Time * severity_lab + (1|study_id), REML = F,
                                           data = .x %>% dplyr::filter(Time!="D10"))),
         lme.tidy = purrr::map(lme.res, ~ broom.mixed::tidy(.)),
         #posthoc.time = purrr::map(lme.res, ~ summary(contrast(emmeans(., ~ Time), method = "pairwise")) %>% tibble()),
         posthoc.time_exposure = purrr::map(lme.res, ~ summary(contrast(emmeans(., ~ Time * severity_lab), method = "pairwise")) %>% tibble())
         )

g_vs_conv_padj <- g_vs_conv %>% 
  unnest(cols="posthoc.time_exposure") %>% 
  #filter(contrast=="Acute severe - M12 severe") %>% 
  filter(contrast %in%c("Acute severe - M12 severe",
                        "Acute moderate - M12 moderate",
                        "Acute mild - M12 mild")) %>% 
      transmute(Assay, UniProt, contrast, estimate,SE,df,t.ratio,p.value) %>% 
  #filter(contrast=="Acute primary_infected - Acute previously_exposed") %>% 
  ungroup() %>% 
    group_by(contrast) %>% 
  mutate(p.adj = p.adjust(p.value, method="fdr"),
                  FDR = ifelse(p.adj <= 0.01, TRUE,FALSE)) %>% 
    ungroup() %>% 
  arrange(p.adj)



(severity_groups_conv_volc <- g_vs_conv_padj %>% 
  group_by(contrast) %>% 
  mutate(severity_lab = case_when(grepl("severe",contrast) ~ "severe",
                                    grepl("moderate",contrast) ~ "moderate",
                                    grepl("mild",contrast) ~ "mild",
                                    .default = NA),
         severity_lab = factor(severity_lab, levels=c("severe","moderate","mild")),
         sig_col = case_when(FDR==T ~ severity_lab,
                             .default = NA)) %>% 
  #slice_max(order_by = estimate, n=1) %>% 
    ggplot(aes(x=severity_lab, y= estimate, color=sig_col)) +
    geom_jitter(width=.1,alpha=.2, show.legend = F,size=.5, shape=16) +
    ggrepel::geom_text_repel(data= . %>% 
                               group_by(severity_lab) %>% slice_max(n=8,order_by = estimate), aes(label=Assay), show.legend = F,force = .5,
                             segment.size=0.2,
                            segment.alpha=.1,
                            size=1.5,max.overlaps = 15, color="gray35") +
    ggrepel::geom_text_repel(data= . %>% 
                               group_by(severity_lab) %>% slice_min(n=8,order_by = estimate), aes(label=Assay), show.legend = F,force = .5,
                             segment.size=0.2,
                            segment.alpha=.1,
                            size=1.5, max.overlaps = 15, color="gray35") +
    geom_hline(yintercept=0, 
               linetype = 3) +
    scale_color_manual(values = patient_kclust3_lab,na.value = "grey") +
    labs(x=NULL,
         title="Each group vs convalecence",
         subtitle = "mixed effect model approach - acute_severity vs m12_severity",
         caption="FDR < 0.01"))

Figure 4E

require(UpSetR) # https://cran.r-project.org/web/packages/UpSetR/vignettes/basic.usage.html

g_vs_conv_padj_tmp.list <- g_vs_conv_padj %>% 
  group_by(contrast) %>% 
  mutate(severity_lab = case_when(grepl("severe",contrast) ~ "severe",
                                    grepl("moderate",contrast) ~ "moderate",
                                    grepl("mild",contrast) ~ "mild",
                                    .default = NA),
         severity_lab = factor(severity_lab, levels=c("severe","moderate","mild")),
         sig_col = case_when(FDR==T ~ severity_lab,
                             .default = NA)) %>%
    filter(estimate>1) %>% 
  group_by(severity_lab) %>%
  summarise(list = list(Assay)) %>%
  mutate(list = setNames(list, severity_lab)) %>%
  pull(list)

severe_log1 <- intersect(setdiff(g_vs_conv_padj_tmp.list$severe, g_vs_conv_padj_tmp.list$mild),
                         setdiff(g_vs_conv_padj_tmp.list$severe, g_vs_conv_padj_tmp.list$moderate))

pdf(paste0(result.tmp.dir,"severity_daps_upset.pdf"),width = 7, height = 3) 
(UpSetR::upset(fromList(g_vs_conv_padj_tmp.list),
              order.by = "freq",point.size = 2,
              text.scale = 1.2,
             #mb.ratio = c(0.6, 0.4),
              sets.bar.color = c("severe" = "#ca0020","moderate" = "#f4a582", "mild" = "#92c5de"),
              keep.order = TRUE,
              mainbar.y.label = "Number of Proteins", 
              sets.x.label = "Proteins per group"))
dev.off()

## quartz_off_screen 
##                 2

Supplementary Table S3

library(gtsummary)
(severityTable <- subjectTable %>% 
  mutate(wbc_count = as.numeric(wbc_count),
         sat = as.numeric(sat)) %>% 
  left_join(patient_clust, by="study_id") %>% 
    tbl_summary(include = c(inf_rbc_max,
                            crp_max,
                            bili_max,
                            crea_max,
                            sat,
                            resp_rate_max,
                            syst_bp_min,
                            plt_count_min,
                            hb_min),
              by = severity_lab, # split table by group
              statistic = list(
                all_continuous() ~ "{median} ({min}-{max})",
                all_categorical() ~ "{n} / {N} ({p}%)"
              ),
              digits = all_continuous() ~ 2,
              missing_text = "(Missing)") %>% 
  add_n() %>% # add column with total number of non-missing observations
  add_p() %>% # test for a difference between groups
  modify_header(label = "**Variable**") %>% # update the column header
  bold_labels())

Variable	N	severe, N = 231	moderate, N = 331	mild, N = 161	p-value2
inf_rbc_max	72	1.20 (0.01-8.00)	0.90 (0.10-5.00)	0.25 (0.01-1.80)	0.042
crp_max	72	208.00 (88.00-381.00)	143.00 (28.00-266.00)	91.50 (14.00-246.00)	<0.001
bili_max	64	25.00 (12.00-135.00)	19.00 (10.00-100.00)	19.00 (5.00-173.00)	0.093
(Missing)		0	4	4
crea_max	72	106.00 (68.00-828.00)	94.00 (47.00-142.00)	84.00 (49.00-122.00)	0.2
sat	72				>0.9
92		0 / 23 (0%)	1 / 33 (3.0%)	1 / 16 (6.3%)
93		1 / 23 (4.3%)	1 / 33 (3.0%)	0 / 16 (0%)
94		0 / 23 (0%)	1 / 33 (3.0%)	0 / 16 (0%)
95		2 / 23 (8.7%)	4 / 33 (12%)	2 / 16 (13%)
96		2 / 23 (8.7%)	3 / 33 (9.1%)	0 / 16 (0%)
97		4 / 23 (17%)	3 / 33 (9.1%)	4 / 16 (25%)
98		8 / 23 (35%)	9 / 33 (27%)	5 / 16 (31%)
99		4 / 23 (17%)	5 / 33 (15%)	3 / 16 (19%)
100		2 / 23 (8.7%)	6 / 33 (18%)	1 / 16 (6.3%)
resp_rate_max	72	20.00 (14.00-48.00)	20.00 (12.00-42.00)	16.00 (13.00-32.00)	0.058
syst_bp_min	72	100.00 (70.00-130.00)	108.00 (76.00-139.00)	108.00 (90.00-125.00)	0.2
plt_count_min	71	38.00 (14.00-112.00)	72.50 (28.00-134.00)	104.00 (51.00-183.00)	<0.001
(Missing)		0	1	0
hb_min	72	115.00 (64.00-157.00)	119.00 (66.00-165.00)	114.00 (66.00-159.00)	0.8
1 Median (Minimum-Maximum); n / N (%)
2 Kruskal-Wallis rank sum test; Fisher’s exact test

subjectTable %>% 
  mutate(wbc_count = as.numeric(wbc_count),
         sat = as.numeric(sat)) %>% 
  left_join(patient_clust, by="study_id") %>% 
  transmute(study_id, 
            severity_lab,
            diff_acuteSample_treatment,diff_acuteSample_treatment.abs,
            diff_acuteSample_spt_current,diff_acuteSample_spt_current.abs) %>% 
  pivot_longer(cols = -c(study_id,severity_lab)) %>% 

compare_means(
    value ~ severity_lab, data = ., group.by = "name",
    method = "wilcox.test")

## # A tibble: 12 × 9
##    name                 .y.   group1 group2     p p.adj p.format p.signif method
##    <chr>                <chr> <chr>  <chr>  <dbl> <dbl> <chr>    <chr>    <chr> 
##  1 diff_acuteSample_tr… value severe moder… 0.875     1 0.88     ns       Wilco…
##  2 diff_acuteSample_tr… value severe mild   0.286     1 0.29     ns       Wilco…
##  3 diff_acuteSample_tr… value moder… mild   0.244     1 0.24     ns       Wilco…
##  4 diff_acuteSample_tr… value severe moder… 0.933     1 0.93     ns       Wilco…
##  5 diff_acuteSample_tr… value severe mild   0.286     1 0.29     ns       Wilco…
##  6 diff_acuteSample_tr… value moder… mild   0.322     1 0.32     ns       Wilco…
##  7 diff_acuteSample_sp… value severe moder… 0.626     1 0.63     ns       Wilco…
##  8 diff_acuteSample_sp… value severe mild   0.755     1 0.76     ns       Wilco…
##  9 diff_acuteSample_sp… value moder… mild   0.379     1 0.38     ns       Wilco…
## 10 diff_acuteSample_sp… value severe moder… 0.626     1 0.63     ns       Wilco…
## 11 diff_acuteSample_sp… value severe mild   0.755     1 0.76     ns       Wilco…
## 12 diff_acuteSample_sp… value moder… mild   0.379     1 0.38     ns       Wilco…

Supplemementary Table S4

#clin.data.severity.groups.new.data %>%
 # write_tsv(paste0(result.dir,"Supplementary_TableS4_ClinicalChemistry_severity_groups.tsv"))

clin.data.severity.groups.new.data %>% head()

## # A tibble: 6 × 7
##   name     group1   group2          p p.adj p.signif method  
##   <fct>    <chr>    <chr>       <dbl> <dbl> <chr>    <chr>   
## 1 crp_max  severe   moderate 0.00237  0.076 **       Wilcoxon
## 2 crp_max  severe   mild     0.000495 0.017 ***      Wilcoxon
## 3 crp_max  moderate mild     0.0963   1     ns       Wilcoxon
## 4 crea_max severe   moderate 0.177    1     ns       Wilcoxon
## 5 crea_max severe   mild     0.0863   1     ns       Wilcoxon
## 6 crea_max moderate mild     0.550    1     ns       Wilcoxon

Figure S8A

prot.input <- prot.data.4.corr %>% column_to_rownames("study_id")
clin.input <- clin.data.4.corr %>% dplyr::select(study_id,c(plt_count_min,inf_rbc_max,crp_max,hb_min,bili_max,crea_max,p_alat,p_asat)) %>% #,contains("SOFA")) %>%
  column_to_rownames("study_id")

cor.res <- prot.input[rownames(clin.input),] %>% 
  correlation::correlation(data2 = clin.input,
                           method = "spearman", 
                           redundant = F, 
                           p_adjust = "fdr") %>% 
  tibble()

df <- cor.res %>%
  filter(n_Obs >= 37, 
         p<=0.05,
         abs(rho)>=0.45
         ) %>% 
  transmute(from=Parameter2, 
            to=Parameter1,
            value=rho) %>% 
  group_by(to) %>% 
  mutate(n_prot =n()) %>% 
  ungroup() %>% 
  group_by(from) %>% 
  mutate(n_clin = n()) %>% 
  ungroup() %>% 
  arrange(desc(n_prot),n_clin) %>% 
   mutate(from = case_when(from=="crp_max"~"CRP",
                          from=="p_alat"~"ALT",
                          from=="p_asat"~"AST",
                          from=="plt_count_min"~"Platelets",
                          from=="inf_rbc_max" ~"Parasitemia",
                          from=="bili_max"~"Bilirubin",
                          from=="hb_min" ~"Hemoglobin",
                          from=="crea_max"~"Creatinine",
                          .default=from)) 
  
df

## # A tibble: 163 × 5
##    from  to    value n_prot n_clin
##    <chr> <chr> <dbl>  <int>  <int>
##  1 CRP   CTSL  0.471      3     22
##  2 CRP   ICAM1 0.489      3     22
##  3 CRP   KYNU  0.467      3     22
##  4 CRP   PTS   0.462      3     22
##  5 CRP   PVR   0.450      3     22
##  6 ALT   CTSL  0.463      3     33
##  7 ALT   ICAM1 0.557      3     33
##  8 ALT   KYNU  0.467      3     33
##  9 ALT   PTS   0.525      3     33
## 10 ALT   PVR   0.528      3     33
## # ℹ 153 more rows

#string <- unique(df$from) 
#string <- setdiff(unique(df$from),names(clin_marker_cols))
#col.grid_clin <- setNames(sample(brewer.pal(length(string),name="Set1")),string)

string_proteins <- unique(df$to)
col.grid.prot <- setNames(rep("grey80",length(string_proteins)), string_proteins)



col.grid <- c(clin_marker_cols,
              #col.grid_clin, 
              col.grid.prot)

## highlight
# three-column data frame in which the first two columns correspond to row names and column names in the matrix, and the third column corresponds to the graphic parameters
border_df = data.frame(c("Parasitemia"), c("CALCA"), c(1))


pdf(paste0(result.tmp.dir,"chordDiagram.pdf")) #width 6.9

circos.par(gap.after = c(rep(1, length(unique(df[[1]]))-1), 15, 
                         rep(1, length(unique(df[[2]]))-1), 15))
chordDiagram(df,
            #  big.gap = 25,
             grid.col = col.grid,
             #annotationTrack = "grid",
                        big.gap = 10,
            small.gap = 1,
link.border = border_df,
             annotationTrack = NULL,
             preAllocateTracks = list(track.height = .1))#max(strwidth(unlist(dimnames(df))))))
circos.track(track.index = 1, panel.fun = function(x, y) {
  circos.text(CELL_META$xcenter, 
              CELL_META$ylim[1],
              CELL_META$sector.index,
              facing = "clockwise",
              cex = 0.6,
              niceFacing = TRUE, 
              adj = c(0, 0.9))
},
bg.border = NA)

#
dev.off()

## quartz_off_screen 
##                 2

circos.clear()

Figure 5

Identification of severity-associated plasma proteomic profiles

## WGCNA
## https://bioinformaticsworkbook.org/tutorials/wgcna.html#gsc.tab=0
#install.packages("BiocManager")
#BiocManager::install("WGCNA")

## data wrangling
selected.assays.wcna <- dap.res %>% filter(p.adj <= 0.01) %>% pull(Assay)

## requires: rows = treatments and columns = gene probes
input_mat <- data.wide %>% 
  inner_join(sampleTable_simple %>% dplyr::select(DAid,study_id,Time, sample_id),by="sample_id") %>% 
  inner_join(subjectTable %>% dplyr::select(study_id),by="study_id") %>% 
  filter(Time=="Acute") %>% 
  column_to_rownames("sample_id") %>% 
  ## restricting to proteins, significant abundant over convalescence (m12 samples)
  dplyr::select(selected.assays.wcna) %>% 
  as.matrix() %>%
  scale()

input_mat[1:5,1:10]

##                   TNFRSF8       IL10      CXCL9        CD74   TNFRSF1B
## 2011PT01|Acute -0.7370011 -1.1852994 -1.4157459  0.08771475 -1.9048313
## 2011PT04|Acute -0.6779312  0.3667134 -0.0943544 -0.19212623  0.2678492
## 2011PT05|Acute  0.1403045  1.0528265  0.5657621  1.29297919  0.3504350
## 2011PT06|Acute  0.2332304 -1.7527932 -1.0945056 -0.41377242 -0.4221094
## 2011PT07|Acute  0.9822293  1.4187290  0.7498430  1.43859264  1.2466066
##                     VCAM1     PLA2G2A     IL18BP       CSF1     B4GALT1
## 2011PT01|Acute -1.1412591 -1.01940457 -1.4608293 -1.6021606 -0.54555371
## 2011PT04|Acute -0.3286294  0.09020523 -0.5969576 -0.3028854 -0.45244260
## 2011PT05|Acute  0.4595043  0.74644622  0.5612046  0.1410837  1.00463269
## 2011PT06|Acute -0.2196398  0.29812935 -0.9891447 -0.5298451  0.04218177
## 2011PT07|Acute  0.9852817  1.00324357  1.1329858  1.2435433  1.42461678

dim(input_mat)

## [1]  72 692

Set up

allowWGCNAThreads()          # allow multi-threading (optional)

## Allowing multi-threading with up to 10 threads.

#> Allowing multi-threading with up to 4 threads.

# Choose a set of soft-thresholding powers
powers = c(c(1:10), seq(from = 12, to = 20, by = 2))

# Call the network topology analysis function
sft = pickSoftThreshold(input_mat,             # <= Input data
                        #blockSize = 30,
                        powerVector = powers,
                        verbose = 5
)

## pickSoftThreshold: will use block size 692.
##  pickSoftThreshold: calculating connectivity for given powers...
##    ..working on genes 1 through 692 of 692
##    Power SFT.R.sq  slope truncated.R.sq  mean.k. median.k. max.k.
## 1      1   0.0296 -0.367          0.729 159.0000  1.58e+02 283.00
## 2      2   0.4780 -1.210          0.871  57.1000  5.25e+01 154.00
## 3      3   0.6850 -1.480          0.924  25.5000  2.07e+01  94.80
## 4      4   0.7540 -1.640          0.955  13.0000  9.36e+00  62.40
## 5      5   0.7920 -1.700          0.970   7.2400  4.50e+00  42.90
## 6      6   0.8230 -1.730          0.960   4.3100  2.34e+00  30.60
## 7      7   0.8240 -1.780          0.920   2.6900  1.27e+00  22.40
## 8      8   0.8640 -1.770          0.973   1.7600  7.56e-01  16.80
## 9      9   0.8850 -1.780          0.962   1.1800  4.33e-01  12.80
## 10    10   0.8950 -1.760          0.951   0.8200  2.78e-01   9.90
## 11    12   0.2970 -2.640          0.140   0.4230  1.07e-01   6.19
## 12    14   0.3330 -3.490          0.324   0.2360  4.37e-02   4.03
## 13    16   0.3400 -3.470          0.314   0.1400  1.93e-02   2.72
## 14    18   0.3360 -3.350          0.298   0.0883  8.49e-03   1.91
## 15    20   0.3310 -3.240          0.306   0.0582  4.06e-03   1.43

#sft$powerEstimate

#### Scale independence & mean connectivity

sft_tibble <- as_tibble(sft$fitIndices)

plot.si <- sft_tibble %>% 
  ggplot(aes(x=Power,
             y=-sign(slope)*SFT.R.sq)) +
  geom_point() +
  geom_label(aes(label=Power)) +
  geom_hline(yintercept = 0.9, color="darkred") +
  theme_minimal() +
  labs(title = "Scale independence",
       y="Scale Free Topology Model fit\n signed R^2",
       x= "Soft Threshold (power")

plot.meank <- sft_tibble %>% 
  ggplot(aes(x=Power,
             y=mean.k.)) +
    geom_label(aes(label=Power)) +
    theme_minimal() +
  labs(title="Mean connectivity",
       x="Soft Threshold (power)",
       y="Mean Connectivity")

plot.si + plot.meank

##Build co-expression network

picked_power = 6#sft$powerEstimate#6
temp_cor <- cor       
cor <- WGCNA::cor         # Force it to use WGCNA cor function (fix a namespace conflict issue)
netwk <- blockwiseModules(input_mat,  # <= input here
                          # == Adjacency Function ==
                          power = picked_power,  # <= power here
                          networkType = "signed",#"signed hybrid",#"signed",
                          # == Tree and Block Options ==
                          deepSplit = 4, #sensitive module detection should be to module splitting, 0 least and 4 most sensitive
                          pamRespectsDendro = F,
                          # detectCutHeight = 0.75,
                          minModuleSize = 30, 
                          maxBlockSize =ncol(input_mat),#4000, 
                          # == Module Adjustments ==
                          reassignThreshold = 0,
                          mergeCutHeight = 0.25,
                          # == TOM == Archive the run results in TOM file (saves time)
                          saveTOMs = T,
                          saveTOMFileBase = "ER",
                          # == Output Options
                          numericLabels = T,
                          verbose = 3)

##  Calculating module eigengenes block-wise from all genes
##    Flagging genes and samples with too many missing values...
##     ..step 1
##  ..Working on block 1 .
##     TOM calculation: adjacency..
##     ..will use 10 parallel threads.
##      Fraction of slow calculations: 0.000000
##     ..connectivity..
##     ..matrix multiplication (system BLAS)..
##     ..normalization..
##     ..done.
##    ..saving TOM for block 1 into file ER-block.1.RData
##  ....clustering..
##  ....detecting modules..
##  ....calculating module eigengenes..
##  ....checking kME in modules..
##      ..removing 84 genes from module 1 because their KME is too low.
##      ..removing 5 genes from module 2 because their KME is too low.
##      ..removing 11 genes from module 3 because their KME is too low.
##      ..removing 1 genes from module 4 because their KME is too low.
##  ..merging modules that are too close..
##      mergeCloseModules: Merging modules whose distance is less than 0.25
##        Calculating new MEs...

cor <- temp_cor     # Return cor function to original namespace

##### Cluster Dendrogram
# Convert labels to colors for plotting
mergedColors = labels2colors(netwk$colors)
# Plot the dendrogram and the module colors underneath
(cluster_dendro <- plotDendroAndColors(
  netwk$dendrograms[[1]],
  mergedColors[netwk$blockGenes[[1]]],
  "Module colors",
  dendroLabels = FALSE,
  hang = 0.03,
  addGuide = TRUE,
  guideHang = 0.05 ))

## $mar
## [1] 1 5 0 1

module_df <- data.frame(
  assay_id = names(netwk$colors),
  Assay = gsub("\\_.*","",names(netwk$colors)),
  colors = labels2colors(netwk$colors)
)

module_df[1:5,]

##   assay_id    Assay    colors
## 1  TNFRSF8  TNFRSF8 turquoise
## 2     IL10     IL10     brown
## 3    CXCL9    CXCL9     brown
## 4     CD74     CD74     brown
## 5 TNFRSF1B TNFRSF1B turquoise

tmp <- unique(module_df$colors)
module.cols <- setNames(tmp, tmp)

Supplementary Figure 9

Figure S9A

## how many proteis in each module
(module_overview <- module_df %>% 
  group_by(colors) %>% 
  count() %>% 
  
  ggplot(aes(x = fct_reorder(colors,-n), y = n, fill = colors, label = n)) +
         geom_bar(stat = "summary", position = "dodge", show.legend = F) +
  geom_text(stat = "sum", vjust = -0.5,show.legend = F, size=2) +
  scale_y_continuous(#limits=c(0,300),
                     expand = c(0, 20)) +
   scale_x_discrete(expand = c(0,-1)) +
  scale_fill_manual(values=module.cols) +
  theme_minimal() +
  theme(axis.text.x = element_blank(),
    axis.text = element_text(size=6), 
    axis.title = element_text(size=6), 
    axis.ticks.x = element_blank()
    ) + 
  labs(title = "WGCNA analysis - protein network modules",
       subtitle = paste0("based on ",dim(input_mat)[2]," proteins (differential abundant proteins)\n",
                         "profiled in ",dim(input_mat)[1]," acute malaria samples"),
       x="WGCNA protein modules",
       y="n Proteins") 
)

#### generate and export networks for all modules

assays_of_interest = module_df #%>%
  #subset(colors %in% c("turquoise"))

npx_of_interest = input_mat[,assays_of_interest$assay_id]
npx_of_interest[1:5,1:5]

##                   TNFRSF8       IL10      CXCL9        CD74   TNFRSF1B
## 2011PT01|Acute -0.7370011 -1.1852994 -1.4157459  0.08771475 -1.9048313
## 2011PT04|Acute -0.6779312  0.3667134 -0.0943544 -0.19212623  0.2678492
## 2011PT05|Acute  0.1403045  1.0528265  0.5657621  1.29297919  0.3504350
## 2011PT06|Acute  0.2332304 -1.7527932 -1.0945056 -0.41377242 -0.4221094
## 2011PT07|Acute  0.9822293  1.4187290  0.7498430  1.43859264  1.2466066

## columns: Assays
## rows: sample_id

TOM = TOMsimilarityFromExpr(npx_of_interest,
                            power = picked_power)

## TOM calculation: adjacency..
## ..will use 10 parallel threads.
##  Fraction of slow calculations: 0.000000
## ..connectivity..
## ..matrix multiplication (system BLAS)..
## ..normalization..
## ..done.

# Add gene names to row and columns
row.names(TOM) = colnames(npx_of_interest)
colnames(TOM) = colnames(npx_of_interest)

edge_list = data.frame(TOM) %>%
  rownames_to_column("Assay1") %>% 
  pivot_longer(cols=-Assay1,names_to = "Assay2",values_to = "adjacency") %>% 
  distinct() %>%
    filter(Assay1!=Assay2) %>% 
  right_join(module_df %>% transmute(module1 = colors,
                                     Assay1 = Assay)) %>% 
  right_join(module_df %>% transmute(module2 = colors,
                                     Assay2 = Assay)) %>% 
  na.omit()

Figure 5A

##Heatmap - protein adjacency

mat <- cor(npx_of_interest, method = "pearson")
row.anno.df <- data.frame(assay_id = rownames(mat)) %>% left_join(module_df) %>% dplyr::rename(Module = colors) 

(assay_adj_hm <- mat %>% 
  Heatmap(name="protein-protein correlation r",
          right_annotation = HeatmapAnnotation(df = row.anno.df %>% transmute(Module),
                                               col = list(Module = module.cols), 
                                               which = "row",
                                               simple_anno_size = unit(1, "mm"),
                                               show_annotation_name = F,
                                               annotation_name_rot = 0,
                                               annotation_name_gp = gpar(fontsize=6),

                                               annotation_name_side = "top",
                                               show_legend = F,
                                               annotation_legend_param = list(title_gp = gpar(fontsize = 6), 
                                                                              labels_gp = gpar(fontsize = 6))),
          row_split = row.anno.df$Module,
          column_split = row.anno.df$Module,
          row_gap = unit(0, "mm"),
          column_gap = unit(0, "mm"), 
          row_dend_width = unit(3, "mm"),
          row_dend_gp = gpar(lwd=.1),
          column_dend_gp = gpar(lwd=.1),
          column_dend_height = unit(3, "mm"), 
          border = TRUE,
          border_gp = gpar(lwd=.1),
          column_title = NULL,
          row_title = NULL,
          show_row_names = F,
          show_column_names = F,
          heatmap_legend_param = list(labels_gp = gpar(fontsize = 6),
                                      title_gp = gpar(fontsize = 6),
                                      direction = "horizontal",
                                      legend_width = unit(2, "cm"),
                                      grid_height = unit(.2, "cm"))
          ))

# Get Module Eigengenes per cluster
MEs0 <- moduleEigengenes(input_mat, mergedColors)$eigengenes

# Reorder modules so similar modules are next to each other
MEs0 <- orderMEs(MEs0)
module_order = names(MEs0) %>% gsub("ME","", .)

# Add treatment names
#MEs0$DAid <- row.names(MEs0)

# tidy data
mME <- MEs0 %>%
  rownames_to_column("sample_id") %>% 
  pivot_longer(names_to = "module", values_to = "module_eigengenes" ,cols = -sample_id) %>%
      separate(sample_id, "\\|", into = c("study_id","Time"),remove = F) %>% 
  mutate(module = gsub("ME", "", module),
         module = factor(module, levels = module_order)) %>% 
  inner_join(subjectTable, 
             by="study_id") 

Figure 5B

## Module-trait relationship

corr_module_eigengene_meta_res <- mME %>% 
  dplyr::select(module, module_eigengenes,contains("SOFA")) %>% 
  group_by(module) %>% 
  correlation(p_adjust = "fdr") 

df <- tibble(corr_module_eigengene_meta_res) %>% 
  filter(Parameter1=="module_eigengenes") %>% 
    mutate(r4fill = case_when(p>0.05 ~ 0,
                              .default=r))  
(module_trait_plot <- ggplot(data = df, 
                             aes(x=Parameter2, y=Group, fill=r4fill,lable=r)) +
    geom_tile() +
    geom_text(aes(label = paste0(r %>% round(2)),
                  color = ifelse(r4fill==0, "grey20", "black")),
              size=1) +
    scale_colour_identity() +
    theme_bw() +
    scale_fill_gradient2(
      low = "blue",
      high = "red",
      mid = "white",
      midpoint = 0,
      limit = c(-1,1)) +
    labs(title = "Module-trait Relationships",
         y="WGCNA modules",
         x = NULL, 
         fill="rho") +
    theme(#axis.text.y = element_text(color= rev(c("yellow","turquoise","red","grey","green","brown","blue"))),
      axis.text.y = element_text(color= rev(c("yellow","turquoise","red","grey","green","brown","blue"))),
          axis.text.x = element_text(angle=45, hjust=1)))

#### Module membership

###  Get Module Eigengenes per cluster
MEs <- moduleEigengenes(input_mat, mergedColors)$eigengenes

## calculate Module membership
geneModuleMembership <- as.data.frame(cor(input_mat, MEs, use = "p")) 

geneModuleMembership.tidy <- geneModuleMembership %>%
  rownames_to_column("Assay") %>% 
  pivot_longer(cols = -Assay) %>% 
  transmute(Assay,
            Module = str_remove(name, "ME"),
            gMM = value)

## calculate pvalue for geneModuleMembership
MMPvalue.tidy <- as.data.frame(corPvalueStudent(as.matrix(geneModuleMembership), nrow(input_mat))) %>%
  rownames_to_column("Assay") %>% 
  pivot_longer(cols = -Assay) %>% 
  transmute(Assay,
            Module = str_remove(name, "ME"),
            pvalue = value) 

gMM.tidy <- geneModuleMembership.tidy %>% right_join(MMPvalue.tidy,by=c("Assay","Module")) 

module_specific_MM <- module_df %>% 
  transmute(Assay,
            Module = colors) %>% 
  inner_join(gMM.tidy)

Supplementary Figur S8B

(turquoise_module_restrictions_density <- module_specific_MM %>% 
   mutate("-log10(pvalue)" = -log10(pvalue)) %>% 
   pivot_longer(cols = c(gMM,"-log10(pvalue)")) %>% 
   mutate(name_label = case_when(name=="gMM"~"threshold > 0.6",
                                 name=="-log10(pvalue)"~"threshold < 0.05",
                                 .default = NA),
          name_label = factor(name_label),
          cutoff = case_when(name=="gMM"~ 0.6,#0.75,
                             name=="-log10(pvalue)"~ -log10(0.05),
                             .default = NA),
          cutoff_pos_y = case_when(name=="gMM"~ 1,
                                   name=="-log10(pvalue)"~ 0.04,
                                   .default = NA)
   ) %>% 
   ggplot(aes(x=value)) +
   geom_density(show.legend = F,linewidth=.2,fill="turquoise") +
   theme_minimal() +
   facet_wrap(~name, ncol = 1,labeller = labeller(name=c("gMM" = "Module membership", "-log10(pvalue)" = "-log10(pvalue)")),scales = "free") +
   geom_vline(aes(xintercept=cutoff),linetype="dashed") +
   geom_text(aes(x=cutoff,
                 y=cutoff_pos_y,
                 label=name_label), 
             size=1,
             check_overlap = TRUE) +
   labs(y="density",
        x=""))

Figure 5C

restricted_module_turquoise <- module_specific_MM %>% 
  filter(Module=="turquoise",
         gMM > 0.6,#0.75,
         pvalue < 0.05
         ) %>% 
  arrange(-pvalue) %>% 
  pull(Assay) 

length(restricted_module_turquoise)

## [1] 161

data.frame(Assay = restricted_module_turquoise) %>% 
  left_join(dap.res %>% 
              transmute(Assay, UniProt)) %>%
  transmute(UniProt) %>% 
  write_tsv(paste0(result.tmp.dir,"restricted_module_turquoise.tsv"))
  #head()

##Online reactome
reactome_result<- read_delim("../Manuscript/20250226_restricted_module_turquoise_ReactomeORA_Result.txt") %>% janitor::clean_names()


(reactome_ora <- reactome_result %>% 
  arrange(entities_fdr) %>% 
  head(n=10) %>% 
    mutate(facet_lab = "turquoise module") %>% 

   ggplot(aes(x=fct_reorder(pathway_name,-log10(entities_fdr)), 
              y=-log10(entities_fdr))) +

    geom_bar(stat = "identity", width = 0.1) +
    geom_point(aes(color=-log10(entities_fdr)),
               size=2) +
    geom_text(aes(label=number_entities_found),
              size=2, nudge_y = .1, color="black")+
    scale_y_continuous(trans="log10") +
    scale_x_discrete(labels = function(x) str_wrap(x, width = 45)) +
        scale_color_viridis() +
    theme_minimal() +
    theme(text = element_text(size=6 ),
          axis.text.y = element_text(size = 6),
          axis.ticks.x = element_blank()) +
    coord_flip() +
    facet_grid(~facet_lab) +
    guides(size = guide_legend(reverse=TRUE),
           ) +
     labs(title = "Reactome database v86",
       color="-log10\n(FDR)",
       y="-log10(FDR)",
       x=NULL)
)

Figure 5D

wrapper <- function(x, ...) 
{
  paste(strwrap(x, ...), collapse = "\n")
}

a = "Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell"
df <- reactome_result %>% 
  arrange(entities_fdr) %>% 
  head(n=10) %>% 
  filter(pathway_name==a) %>% 
  transmute(pathway_name, submitted_entities_found) %>% 
  separate_rows(submitted_entities_found, sep=";\\s*") %>% 
  left_join(
    data.long %>% inner_join(sampleTable_simple, by="sample_id") %>% transmute(Assay,NPX,UniProt,sample_id,study_id,Time) %>% filter(Time=="Acute"),
    by=c("submitted_entities_found"="UniProt")
  ) %>% 
  inner_join(patient_clust,by="study_id")

(reactome_ora_IIBLNL <- df %>%  group_by(Assay, severity_lab) %>% 
    summarise(NPXmean = mean(NPX),
              NPXmedian = median(NPX),
              NPXsd = sd(NPX),
              NPXn = n(),
              NPXse = NPXsd / sqrt(NPXn)
    ) %>% 
    mutate(NPXci95 = NPXse * qt(.975, NPXn - 1)) %>% 
    ggplot(aes(x=Assay, y=NPXmean, group=severity_lab, color=severity_lab)) +
    geom_point(size=.25) +
    geom_polygon(fill=NA, show.legend = F, lwd=0.2) +
    geom_errorbar(aes(x = Assay,
                      ymin=NPXmean-NPXci95, 
                      ymax=NPXmean+NPXci95, ),
                  linewidth=.5, 
                  width=.2,
                  alpha=.5) +
    # Make it circular!
    coord_polar(clip = "off") +
    theme_minimal() +
    labs(x="",
         y="mean (NPX) +- 95% CI",

         title = wrapper(a, width = 40),
                  color="mean (NPX) +- 95% CI") +
    scale_color_manual(values=patient_kclust3_lab) +
    # Annotate the bars and the lollipops so the reader understands the scaling
    annotate(x = 0, y = 0, label = "0", fontface =2, geom = "text", color = "gray12", size = 1.5) +
    annotate(x = 0, y = 1, label = "1", fontface =2, geom = "text", color = "gray12", size = 1.5) +
    annotate(x = 0, y = 2, label = "2", fontface =2, geom = "text", color = "gray12", size = 1.5) +
    annotate(x = 0, y = 3, label = "3", fontface =2, geom = "text", color = "gray12", size = 1.5) +
    theme(
      axis.title = element_blank(),
      axis.ticks = element_blank(),
      axis.text.y = element_blank(),
      axis.text.x = element_text(color = "gray12", size = 4),
      legend.position = "right",
      legend.text = element_text(size=6),
      legend.title = element_text(size=6),
      title = element_text(size=5, face='bold'),
      plot.title = element_text(hjust = 0.5))
  )

a = "Neutrophil degranulation"
df <- reactome_result %>% 
  arrange(entities_fdr) %>% 
  head(n=10) %>% 
  filter(pathway_name==a) %>% 
  transmute(pathway_name, submitted_entities_found) %>% 
  separate_rows(submitted_entities_found, sep=";\\s*") %>% 
  left_join(
    data.long %>% inner_join(sampleTable_simple, by="sample_id") %>% transmute(Assay,NPX,UniProt,sample_id,study_id,Time) %>% filter(Time=="Acute"),
    by=c("submitted_entities_found"="UniProt")
  ) %>% 
  inner_join(patient_clust,by="study_id")

(reactome_ora_ND <- df %>%  group_by(Assay, severity_lab) %>% 
    summarise(NPXmean = mean(NPX),
              NPXmedian = median(NPX),
              NPXsd = sd(NPX),
              NPXn = n(),
              NPXse = NPXsd / sqrt(NPXn)
    ) %>% 
    mutate(NPXci95 = NPXse * qt(.975, NPXn - 1)) %>% 
    ggplot(aes(x=Assay, y=NPXmean, group=severity_lab, color=severity_lab)) +
    geom_point(size=.25) +
    geom_polygon(fill=NA, show.legend = F, lwd=0.2) +
    geom_errorbar(aes(x = Assay,
                      ymin=NPXmean-NPXci95, 
                      ymax=NPXmean+NPXci95, ),
                  linewidth=.5,    
                  width=.2,
                  alpha=.5) +
    # Make it circular!
    coord_polar(clip = "off") +
    theme_minimal() +
    labs(x="",
         title = wrapper(a, width = 40),
                  color="mean (NPX) +- 95% CI") +
    scale_color_manual(values=patient_kclust3_lab) +
    # Annotate the bars and the lollipops so the reader understands the scaling
    annotate(x = 0, y = 0, label = "0", fontface =2, geom = "text", color = "gray12", size = 1.5) +
    annotate(x = 0, y = 1, label = "1", fontface =2, geom = "text", color = "gray12", size = 1.5) +
    annotate(x = 0, y = 2, label = "2", fontface =2, geom = "text", color = "gray12", size = 1.5) +
    annotate(x = 0, y = 3, label = "3", fontface =2, geom = "text", color = "gray12", size = 1.5) +
    theme(
      axis.title = element_blank(),
      axis.ticks = element_blank(),
      axis.text.y = element_blank(),
      axis.text.x = element_text(color = "gray12", size = 4),
      legend.position = "right",
      legend.text = element_text(size=6),
      legend.title = element_text(size=6),
      title = element_text(size=5, face='bold'),
      plot.title = element_text(hjust = 0.5))
  )

a = "TNFR2 non-canonical NF-kB pathway"
df <- reactome_result %>% 
  arrange(entities_fdr) %>% 
  head(n=10) %>% 
  filter(pathway_name==a) %>% 
  transmute(pathway_name, submitted_entities_found) %>% 
  separate_rows(submitted_entities_found, sep=";\\s*") %>% 
  left_join(
    data.long %>% inner_join(sampleTable_simple, by="sample_id") %>% transmute(Assay,NPX,UniProt,sample_id,study_id,Time) %>% filter(Time=="Acute"),
    by=c("submitted_entities_found"="UniProt")
  ) %>% 
  inner_join(patient_clust,by="study_id")

(reactome_ora_TNFR2 <- df %>%  group_by(Assay, severity_lab) %>% 
    summarise(NPXmean = mean(NPX),
              NPXmedian = median(NPX),
              NPXsd = sd(NPX),
              NPXn = n(),
              NPXse = NPXsd / sqrt(NPXn)
    ) %>% 
    mutate(NPXci95 = NPXse * qt(.975, NPXn - 1)) %>% 
    ggplot(aes(x=Assay, y=NPXmean, group=severity_lab, color=severity_lab)) +
    geom_point(size=.25) +
    geom_polygon(fill=NA, show.legend = F, lwd=0.2) +
    geom_errorbar(aes(x = Assay,
                      ymin=NPXmean-NPXci95, 
                      ymax=NPXmean+NPXci95),
                  linewidth=.5,
                  width=.2,
                  alpha=.5) +
    # Make it circular!
    coord_polar(clip = "off") +
    theme_minimal() +
    labs(x=NULL,
         color="mean (NPX) +- 95% CI",
         title = wrapper(a, width = 40)) +
    scale_color_manual(values=patient_kclust3_lab) +
    # Annotate the bars and the lollipops so the reader understands the scaling
    annotate(x = 0, y = 0, label = "0", fontface =2, geom = "text", color = "gray12", size = 1.5) +
    annotate(x = 0, y = 1, label = "1", fontface =2, geom = "text", color = "gray12", size = 1.5) +
    annotate(x = 0, y = 2, label = "2", fontface =2, geom = "text", color = "gray12", size = 1.5) +
    annotate(x = 0, y = 3, label = "3", fontface =2, geom = "text", color = "gray12", size = 1.5) +
  annotate(x = 0, y = 4, label = "4", fontface =2, geom = "text", color = "gray12", size = 1.5) +
    theme(
      axis.ticks = element_blank(),
      axis.title = element_blank(),
      axis.text.y = element_blank(),
      axis.text.x = element_text(color = "gray12", size = 4),
      legend.position = "right",
      legend.text = element_text(size=6),
      legend.title = element_text(size=6),
      title = element_text(size=5, face='bold'),
      plot.title = element_text(hjust = 0.5))
)

Figure 6

Severity-associated profiles of condensed 11- protein signature in malaria and other febrile infections.

library(mixOmics)
data.mo <- df_acute_patclust_incl_conv %>% 
  filter(Assay %in% restricted_module_turquoise) %>% 
  pivot_wider(names_from = Assay, values_from = NPX, id_cols=c(severity_lab,sample_id)) %>% 
  column_to_rownames("sample_id")

X <- data.mo %>% dplyr::select(-c(severity_lab))
Y <- data.mo$severity_lab
#####
data.pca <- mixOmics::pca(X, ncomp=10, center = TRUE, scale = TRUE)
plot(data.pca)

plotIndiv(data.pca, 
          group = Y,
          ind.names = F,
          legend = TRUE, 
          col.per.group = patient_kclust3_lab_conv,
          title = 'PCA on all NPX data')

#####
### PLS-Discriminant Analysis based on severity groups

data.plsda <- mixOmics::plsda(X, Y, ncomp = 10)
# takes a couple of minutes to run
perf.data.plsda <- perf(data.plsda, 
                        validation = "Mfold",
                        folds = 5,
                        progressBar = F,
                        auc = TRUE, 
                        nrepeat = 10) #100
################
(plot(perf.data.plsda, col = color.mixo(1:3), sd = TRUE, legend.position = "horizontal"))

## NULL

######
list.keepX <- c(1:10) # grid of possible keepX values that will be tested for each component
tune.splsda <- tune.splsda(X,
                           Y, 
                           ncomp = 3, 
                           validation = "Mfold",
                           folds = 5, 
                           progressBar = TRUE, 
                           dist = "centroids.dist",
                           measure = "BER",
                           test.keepX = list.keepX, 
                           nrepeat = 10, 
                           cpus = 8)

## 
## comp 1 
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#####
## The classification error rates for each component conditional on the last component are represented below, for all components specified in the tune function.
plot(tune.splsda)

error <- tune.splsda$error.rate  # error rate per component for the keepX grid
ncomp <- tune.splsda$choice.ncomp$ncomp
ncomp

## [1] 1

ncomp = 2
#####
select.keepX <- tune.splsda$choice.keepX[1:ncomp]  # optimal number of variables to select
select.keepX

## comp1 comp2 
##    10     3

#####

splsda.data <- mixOmics::splsda(X, Y, ncomp = ncomp, keepX = select.keepX) 

#####

plotIndiv(splsda.data, 
          comp = c(1,2),
          group = Y, 
          ind.names = F, 
          ellipse = TRUE,
          #col.per.group =  patient_kclust3_lab,
          legend = T, 
          title = 'sPLS-DA on data, comp 1 & 2')

plotLoadings(splsda.data, comp = 1,ndisplay=20, title = 'Loadings on comp 1',legend.color =  patient_kclust3_lab_conv, 
             contrib = 'max', method = 'mean')

plotLoadings(splsda.data, comp = 2,ndisplay = 10, title = 'Loadings on comp 2', legend.color =  patient_kclust3_lab_conv, 
             contrib = 'max', method = 'mean')

auc.splsda <- auroc(splsda.data, roc.comp = 2, print = FALSE) # AUROC for the first component

auc.splsda$graph.Comp1

## NULL

auroc(splsda.data, roc.comp = 1, print = FALSE) 

Figure 6A

splsda.kclust.clusters <- plotIndiv(splsda.data, 
                                 comp = c(1,2),
                                 group = Y, 
                                 ind.names = F, 
                                 ellipse = TRUE,
                                 col.per.group = patient_kclust3_lab_conv,
                                 legend = F, 
                                 title = 'sPLS-DA on data, comp 1 & 2')

(splsda.kclust.clusters.ggplot <- splsda.kclust.clusters$df %>% 
    mutate(group = factor(group, levels=c("severe","moderate","mild","convalescence"))) %>%  
    
    ggplot(aes(x=x,y=y,color=group)) +
    ggforce::geom_mark_ellipse(aes(color = as.factor(group), fill=group),alpha=.1,show.legend = F, expand = unit(0.5,"mm")) +
    geom_point(size=0.5) + 
    scale_color_manual(values=patient_kclust3_lab_conv) +
    scale_fill_manual(values=patient_kclust3_lab_conv) +
    
    theme_minimal() +
    labs(title = "sparse PLS-DA",
         color= NULL,
         x=paste0("X-variate 1: ",round(splsda.data$prop_expl_var$X[[1]]*100,1),"% expl. var"),
         y=paste0("X-variate 2: ",round(splsda.data$prop_expl_var$X[[2]]*100,1),"% expl. var")) +
    theme(legend.position = "right") 
)

Figure 6B

plsda_loadings.df <-   
  data.frame(splsda.data$loadings$X) %>% 
  rownames_to_column("Assay") %>% 
  pivot_longer(names_to = "comp",values_to = "values",cols = -Assay) %>% 
  filter(values != 0,
         comp %in% c("comp1","comp2")) %>% 
  group_by(comp) %>% 
  mutate(values = scales::rescale(values, to=c(-1,1))) %>% 
  ungroup() 

(plsda_loadings.volcano.alt <-  plsda_loadings.df %>% 
    ggplot(aes(x=fct_reorder(Assay,values,.desc = T), y=values, color=comp,fill=comp)) +
    geom_point(size=0.5,alpha=1) +
    geom_col(width = 0.01) +
    coord_flip() +
    theme_minimal() +
    scale_color_manual(values=c(comp1 = "#1f78b4",comp2 = "#b2df8a")) +
    scale_fill_manual(values=c(comp1 = "#1f78b4",comp2 = "#b2df8a")) +
    labs(x="",
         fill=NULL,
         color=NULL,
         y="scaled loading values",
         title="sPLSDA loadings") +
    theme(legend.title = element_text(size=6),
          axis.text.x = element_text(size=6),
          legend.position = "right",
          legend.justification="right", 
          legend.box.spacing = unit(0, "pt")))

malaria.severity.siganture <- data.frame(splsda.data$loadings$X) %>% 
  rownames_to_column("Assay") %>% 
  pivot_longer(names_to = "comp",values_to = "values",cols = -Assay) %>% 
  filter(values != 0,
         comp %in% c("comp1")#,"comp2")
         )

Figure 6C

my_comparisons_severe_conv <- list(c("severe", "moderate"), c("moderate", "mild"), c("severe", "mild"),c("mild","convalescence"))

splsda.c1.top9 <- plsda_loadings.df %>% 
  filter(comp=="comp1") %>% 
  slice_min(n=9, order_by = values) %>% pull(Assay)# %>% 

(splsda.c1.top9 <- df_acute_patclust_incl_conv %>% 

    dplyr::filter(Assay %in% c(splsda.c1.top9)) %>% 
    mutate(Assay = factor(Assay, levels = c(splsda.c1.top9))) %>% 
    ggplot(aes(x=severity_lab, y=NPX, color=severity_lab, fill=severity_lab)) + 
    geom_violin(trim = F,alpha=.9) +
    geom_jitter(size=0.25,show.legend = F, width = 0.05, alpha=1, color="grey20") +
    geom_boxplot(alpha=.7,width=0.25,outlier.shape = NA,color="black", fatten = 2,lwd=.25,show.legend = F) +
    stat_compare_means(method = "wilcox.test",
                       label.sep = "\n",
                       hide.ns = T,
                       label = "p.signif" ,
                       vjust = .5,
                       size=2,
                       lwd = .2,
                       comparisons =my_comparisons_severe_conv,
                       show.legend = F) +
    facet_wrap(~Assay,ncol = 3,scales = "free_y") +
    theme_minimal() +
    theme(legend.position="bottom",
          axis.text.x = element_blank()) +
    labs(x="",
         color=NULL,
         fill=NULL) +
    scale_color_manual(values= patient_kclust3_lab_conv) +
    scale_fill_manual(values= patient_kclust3_lab_conv))

###plsda.selection <- data.frame(splsda.data$loadings$X) %>% 
#  rownames_to_column("Assay") %>% 
#  pivot_longer(names_to = "comp",values_to = "values",cols = -Assay) %>% 
#  filter(values != 0,
#         comp %in% c("comp1","comp2")) %>% 
#  pull(Assay)
plsda.selection <- malaria.severity.siganture %>% pull(Assay)

data.frame(Assay = plsda.selection) %>% 
  left_join(universe.proteins,by="Assay") %>% 
  transmute(Assay, UniProt)# %>% 

##       Assay UniProt
## 1     HMOX1  P09601
## 2     IL2RA  P01589
## 3      CD14  P08571
## 4     ICAM1  P05362
## 5   B4GALT1  P15291
## 6     CDCP1  Q9H5V8
## 7     CALCA  P01258
## 8  TNFRSF1B  P20333
## 9      RRM2  P31350
## 10     LAG3  P18627

  #write_tsv(paste0(result.dir,"MIP_Severity_Protein_signature_uniprotid.tsv"))

Figure 6D

## Explore 1536 data set - MGH Covid-19 study, Filbin et al. 2021

#### Make data ready

# identify proteins with NPX below LOD in more than 70% of samples
assays2rm <- covid_NPXdata %>% 
  mutate(belowLOD = LOD>NPX) %>% 
  group_by(Assay) %>% 
  count(belowLOD,sort=TRUE) %>% 
  filter(belowLOD==T,
         n > length(unique(covid_NPXdata$SampleID))*0.7) %>% 
  pull(Assay)

# remove proteins identified above from data
covid_NPXdata_rm <- covid_NPXdata %>% 
  filter(!Assay%in%assays2rm, Timepoint=="D0") %>%
  dplyr::select(SampleID, subject_id, Assay, NPX, Panel)

# identify proteins with different values in different panels
assays2rm <- covid_NPXdata_rm %>%
  group_by(subject_id, Assay) %>%
  summarise(n = n(), .groups = "drop") %>%
  filter(n > 1L) %>%
  pull(Assay) %>%
  unique()

# one example of the proteins identified above
covid_NPXdata_rm %>% filter(subject_id==1,Assay=="CXCL8")

## # A tibble: 4 × 5
##   SampleID subject_id Assay   NPX Panel          
##   <chr>         <dbl> <chr> <dbl> <chr>          
## 1 1_D0              1 CXCL8  1.46 CARDIOMETABOLIC
## 2 1_D0              1 CXCL8  4.40 INFLAMMATION   
## 3 1_D0              1 CXCL8  4.59 NEUROLOGY      
## 4 1_D0              1 CXCL8  3.52 ONCOLOGY

# convert data to wide format
covid_NPXdata_wide <- covid_NPXdata_rm %>%
  ## values_fn calculates median values for duplicated features (duplicated because part of every olink panel)
  pivot_wider(names_from = Assay, values_from = NPX,id_cols = subject_id, values_fn = median)

# make data ready for GSVA
covid_NPXdata_mat <- covid_NPXdata_wide %>%  
  column_to_rownames("subject_id") %>%
  as.matrix() %>% 
  t()

#### Run single sample gene set enrichment analysis

library(GSVA)

# run ssgsea on signature from sPLSDA
GSE_results <- gsva(expr = covid_NPXdata_mat,
                    gset.idx.list = list(sig=plsda.selection),verbose=F,
                    method="zscore")

#data_plot_sPLSDA <- data.frame(group=as.factor(covid_clinicalData$WHO.0),score=as.vector(GSE_results))

GSEA_result_df <- data.frame(subject_id = colnames(covid_NPXdata_mat),
                             ssES = as.vector(GSE_results)) %>% 
  right_join(mgh.covid.meta %>% transmute(subject_id= as.character(subject_id),
                                          who_0 = as.factor(who_0)), by="subject_id")

# show results
(MGH_covid_ssES <- GSEA_result_df %>% 
  ggplot(aes(x=who_0, y=ssES, fill=who_0)) +
    geom_jitter(width=0.15,size=.3,alpha=.2) +
 # geom_violin(width=1.5, trim = F, alpha=0.7,show.legend = F,lwd=.25) +
  geom_boxplot(width=.3,alpha=.6, fatten = 2,lwd=.25,outlier.colour = NA) +
  #geom_boxplot(alpha=0.6, width=.2, show.legend = F)+
  theme_minimal()+
    theme(legend.position = "none") +
  labs(y="ssES score (zscore)",x="Severity group",fill=""))

Figure 6E

#### Make data ready

MIP.long <- data.long %>% 
  left_join(sampleTable_simple) %>%
  filter(!grepl("D10",sample_id)) %>% 
    left_join(patient_clust) %>% 
  mutate(sample_type = case_when(Time=="Acute" ~ paste0(severity_lab," malaria"),
                                 .default = paste0(#Time,
                                   "Malaria",
                                   " convalescence"))) %>% 
  transmute(sample_id, sample_type, Assay, NPX)


data_tf_mip_wide <- TF.long %>% 
  bind_rows(MIP.long) %>% 
  pivot_wider(names_from = Assay, values_from = NPX, id_cols = c(sample_id,sample_type), values_fn = median) 

all.mat <- data_tf_mip_wide %>%
  dplyr::select(-c(sample_type)) %>% 
  column_to_rownames("sample_id") %>% 
  as.matrix() %>% 
  t()

#### Run single sample gene set enrichment analysis
library(GSVA)
# run ssgsea on signature from sPLSDA
GSE_results <- gsva(expr = all.mat,
                    gset.idx.list = list(sig=plsda.selection),#list(sig=severity_signature_proteins),
                    verbose=F,
                    method="zscore")


GSEA_result_df <- data.frame(sample_id = colnames(all.mat),
                             ssES = as.vector(GSE_results)) %>% 
  left_join(data_tf_mip_wide %>% dplyr::select(sample_id,sample_type), by="sample_id") %>% 
  left_join(
  TF_SOFA %>% transmute(sample_id = paste0(study_id,"|Acute"), SOFA_total) %>%
  bind_rows(
    subjectTable %>% transmute(sample_id = paste0(study_id,"|Acute"), SOFA_total)
  )) %>% 
  mutate(sample_type = case_when(sample_type == "Influensa A" ~ "Influenza A",
                                 sample_type == "Influensa B" ~ "Influenza B",
                                 .default = sample_type))

# show results

(TF_ssES_plot <- GSEA_result_df %>% 
ggplot(aes(x=fct_reorder(sample_type,ssES, median,.desc = T), y=ssES, fill=sample_type)) +
  geom_jitter(width=0.15,size=.3,alpha=.2) +
  geom_boxplot(width=.3,alpha=.6, fatten = 2,lwd=.25,outlier.colour = NA) +
  theme_minimal() +
    scale_fill_manual(values=c("severe malaria"=patient_kclust3_lab[[3]],
                               "moderate malaria"=patient_kclust3_lab[[2]],
                               "mild malaria"=patient_kclust3_lab[[1]],
                               "Malaria convalescence"=patient_kclust3_lab_conv[[4]]),
                      na.value = "#8dd3c7") +
  geom_hline(yintercept = 0,linetype="dotted") +
  labs(title="Evaluation of malaria disease severity signature",
       x=NULL,
       y="Gene Set Variation Analysis\nsingle sample enrichment score\n(zscore)",
       fill="") +
    theme(legend.position = "none") +
      scale_x_discrete(labels = label_wrap(8)) )

Supplementary Table S5

malaria.severity.siganture %>% 
  arrange(values) %>% 
  dplyr::rename(importance = values) %>% 
  head()

## # A tibble: 6 × 3
##   Assay    comp  importance
##   <chr>    <chr>      <dbl>
## 1 TNFRSF1B comp1     -0.611
## 2 B4GALT1  comp1     -0.576
## 3 IL2RA    comp1     -0.391
## 4 ICAM1    comp1     -0.252
## 5 HMOX1    comp1     -0.202
## 6 RRM2     comp1     -0.140

  #write_tsv(paste0(result.dir,"Supplementary_TableS5_SeveritySignature.tsv"))

Supplementary Table S6

TF cohort - sampleTable

##gtsummary
library(gtsummary)

TF_sampleTable %>% 
  dplyr::select(-sample_type) %>% 
  inner_join(GSEA_result_df, by="sample_id") %>% 
  transmute(sample_type, 
            SOFA_total = as.numeric(SOFA_total),
            age = as.numeric(age),
            gender) %>% 
  filter(!grepl("Malaria|malaria", sample_type)) %>% 
  
  tbl_summary(include = c(sample_type, age, gender,
                          SOFA_total),
              by = sample_type,
              statistic = list(all_continuous() ~ "{median} ({min}-{max})",
                               all_categorical() ~ "{n} / {N} ({p}%)"
              ),
              #digits = all_continuous() ~ 2
              digits = c(age ~ 0)
              )

Characteristic	Campylobacter, N = 171	Dengue, N = 191	E.coli -pyelonefriter, N = 91	Influenza A, N = 171	Influenza B, N = 181	Mycoplasma pneumonier, N = 51	Salmonella (only feces), N = 121	Shigella, N = 31
age	32 (26-61)	34 (22-66)	56 (24-87)	45 (23-88)	38 (26-68)	40 (18-72)	38 (22-61)	40 (29-50)
gender	11 / 17 (65%)	11 / 19 (58%)	2 / 9 (22%)	5 / 17 (29%)	7 / 18 (39%)	3 / 5 (60%)	8 / 12 (67%)	1 / 3 (33%)
SOFA_total
0	15 / 17 (88%)	12 / 19 (63%)	4 / 5 (80%)	14 / 17 (82%)	15 / 18 (83%)	3 / 4 (75%)	11 / 12 (92%)	2 / 3 (67%)
1	2 / 17 (12%)	3 / 19 (16%)	0 / 5 (0%)	3 / 17 (18%)	1 / 18 (5.6%)	1 / 4 (25%)	1 / 12 (8.3%)	0 / 3 (0%)
2	0 / 17 (0%)	4 / 19 (21%)	0 / 5 (0%)	0 / 17 (0%)	2 / 18 (11%)	0 / 4 (0%)	0 / 12 (0%)	1 / 3 (33%)
3	0 / 17 (0%)	0 / 19 (0%)	1 / 5 (20%)	0 / 17 (0%)	0 / 18 (0%)	0 / 4 (0%)	0 / 12 (0%)	0 / 3 (0%)
Unknown	0	0	4	0	0	1	0	0
1 Median (Minimum-Maximum); n / N (%)

Figure 7

A protein-centric view on integrated analysis to ascertain immune cell communication associated with disease severity

Figure 7A

similar_modules <- c(restricted_module_turquoise,
                     module_df %>% filter(colors=="brown") %>% pull(Assay),
                     module_df %>% filter(colors=="blue") %>% pull(Assay))
library(eulerr)
euler_plot <- euler(
  list(
    "Differential\nabundant\nproteins\nin\nacute malaria"=selected.assays.wcna,
    "Severity associated\nproteins in plasma" = restricted_module_turquoise)
)

plot(euler_plot,
     fills = c("white",
               "turquoise"),
               
     quantities = TRUE,
     lty = 1,#1:3,
     fontsize=6,
     labels = list(fontsize=5),
     shape = "ellipse") 

Figure 7B

secretome_location_dap_severity <- dap.res %>% 
  filter(Assay %in% restricted_module_turquoise) %>% 
  inner_join(hpa_24.0, by=c("Assay"="gene","UniProt"="uniprot")) %>% 
  mutate(secretome_location_tissue_spec = case_when(secretome_location=="Not secreted"~ paste0(secretome_location," - ",rna_tissue_specificity),
                                                   .default = secretome_location)) %>% 
  group_by(secretome_location_tissue_spec) %>% 
 mutate(n_secretome_location_tissue_spec = n()) #count(sort = TRUE) 


## plot everything
(hpa.protein.origin.overview_severity <- secretome_location_dap_severity %>% 
    ungroup() %>% 
    transmute(secretome_location_tissue_spec = factor(secretome_location_tissue_spec,
                                                     levels = rev(c("Secreted to blood",
                                                                    "Intracellular and membrane",
                                                                    "Secreted in other tissues",
                                                                    "Secreted to extracellular matrix",  
                                                                    "Secreted to digestive system", 
                                                                    "Secreted in brain",
                                                                    "Secreted - unknown location",
                                                                    "Secreted in female reproductive system",
                                                                    "Secreted in male reproductive system",
                                                                    "Not secreted - Tissue enriched", 
                                                                    "Not secreted - Tissue enhanced",
                                                                    "Not secreted - Group enriched",
                                                                    "Not secreted - Low tissue specificity"))),
              n_secretome_location_tissue_spec) %>% 
    distinct() %>% 
    ggplot(aes(x = secretome_location_tissue_spec, y = n_secretome_location_tissue_spec, fill = secretome_location_tissue_spec)) +
    geom_col(width = 0.5) +
    geom_text(aes(label=n_secretome_location_tissue_spec),size=2, nudge_y = -.2) +
    coord_flip() +
    scale_y_continuous(trans="pseudo_log",name = "Number of proteins\nassociated with severity",
                       sec.axis = sec_axis(~.,labels = NULL,breaks = NULL,
                                           #name = "Number of DAPs"
                                           ), 
                       #expand=c(0,.15)
                       expand = c(0,0)
                       ) +
    theme_bw() +
    theme(axis.text.y = element_text(size = 6),
          axis.text.x = element_text(size = 6),
          legend.text=element_text(size=6),
          legend.title=element_text(size=6),
          plot.title = element_text(size=6),
          legend.position = "none")+

    scale_fill_manual(values=secretome_location_tissue_spec_cols,
                      limits = secretome_location_dap.order) +
    labs(fill="Protein\norigin\nby HPA",
         x=NULL))

## plot everything
(hpa.protein.origin.overview_severity <- secretome_location_dap_severity %>% 
    ungroup() %>% 
    transmute(secretome_location_tissue_spec = factor(secretome_location_tissue_spec,
                                                     levels = c("Secreted to blood",
                                                                    "Intracellular and membrane",
                                                                    "Secreted in other tissues",
                                                                    "Secreted to extracellular matrix",  
                                                                    "Secreted to digestive system", 
                                                                    "Secreted in brain",
                                                                    "Secreted - unknown location",
                                                                    "Secreted in female reproductive system",
                                                                    "Secreted in male reproductive system",
                                                                    "Not secreted - Tissue enriched", 
                                                                    "Not secreted - Tissue enhanced",
                                                                    "Not secreted - Group enriched",
                                                                    "Not secreted - Low tissue specificity")),
              n_secretome_location_tissue_spec) %>% 
    distinct() %>% 
    ggplot(aes(x = secretome_location_tissue_spec, y = n_secretome_location_tissue_spec, fill = secretome_location_tissue_spec)) +
    geom_col(width = 0.5) +
    geom_text(aes(label=n_secretome_location_tissue_spec),size=2, nudge_y =1.5) + #0.1
    #coord_flip() +
    scale_y_continuous(#trans="pseudo_log",
                       name = "Number of proteins",
                       sec.axis = sec_axis(~.,labels = NULL,breaks = NULL,
                                           #name = "Number of DAPs"
                                           ), 
                       #expand=c(0,.15)
                       #expand = c(0,0.1),
                       limits = c(0,51)
                       ) +
    theme_bw() +
    theme(axis.text.y = element_text(size = 6),
          axis.text.x = element_text(size = 6,angle=90,hjust = 1,vjust = 0.5),
          #axis.text.x = element_text(size = 6,angle=45,hjust = 1),
          axis.title.y = element_text(size=6),

          legend.text=element_text(size=6),
          legend.title=element_text(size=6),
          plot.title = element_text(size=6),
          legend.position = "none")+

    scale_fill_manual(values=secretome_location_tissue_spec_cols,
                      limits = secretome_location_dap.order) +
    labs(fill="Protein\norigin\nby HPA",
         x=NULL))

Figure 7C

proteins2label <- df_acute_patclust_incl_conv %>% 
  group_by(UniProt,Assay, severity_lab) %>% 
  summarise(NPXmean = mean(NPX),
            NPXmedian = median(NPX),
            NPXsd = sd(NPX),
            NPXn = n(),
            NPXse = NPXsd / sqrt(NPXn)
  ) %>% 
  #ungroup() %>% 
  mutate(NPXci95 = NPXse * qt(.975, NPXn - 1)) %>% 
  left_join(
    secretome_location_dap_severity %>%
    filter(Assay %in% restricted_module_turquoise) %>%
  transmute(Assay,secretome_location_tissue_spec), by="Assay"
  ) %>% 
  filter(severity_lab=="severe",
         Assay %in% restricted_module_turquoise,
         !is.na(secretome_location_tissue_spec)) %>% 
  
  group_by(secretome_location_tissue_spec) %>% 
  #transmute(Assay,NPX, severity_lab, secretome_location_tissue_spec) %>% 
  distinct() %>% 
  slice_max(order_by = NPXmean,n = 3) %>% pull(Assay)

tmp.df <- df_acute_patclust_incl_conv %>% 
  group_by(UniProt,Assay, severity_lab) %>% 
  summarise(NPXmean = mean(NPX),
            NPXmedian = median(NPX),
            NPXsd = sd(NPX),
            NPXn = n(),
            NPXse = NPXsd / sqrt(NPXn)
  ) %>% 
  #ungroup() %>% 
  mutate(NPXci95 = NPXse * qt(.975, NPXn - 1)) %>% 
  filter(Assay%in%restricted_module_turquoise) %>% 
  left_join(
    secretome_location_dap_severity%>% 
      transmute(Assay, secretome_location_tissue_spec), by="Assay")

(turqoise_allProteins_lab <- tmp.df %>% 
  ggplot(aes(x=fct_reorder(Assay,NPXmean,.desc = F), y=NPXmean)) +
  geom_point(shape=16,size=.5,aes(color=severity_lab)) +
  geom_errorbar(aes(x = Assay,#reorder(str_wrap(Assay, 5), estimate),
                    ymin=NPXmean-NPXci95, 
                    ymax=NPXmean+NPXci95,
                    color=severity_lab),
                linewidth=.2,    # Thinner lines
                width=.2,
                alpha=.5) +
  geom_hline(yintercept = 0,lty=5, lwd=.2) +
    ggrepel::geom_text_repel(data = . %>% filter(Assay %in% proteins2label,#c("LGALS9","HAVCR2","IL4","IL4R","CD70","PDCD1","CD274"),
                                                 severity_lab == "severe"),
                             aes(label = Assay, colour=secretome_location_tissue_spec, nudge_y=NPXmean),
                             size = .9,
                             force_pull = 3, # do not pull toward data points
                             force = .15, # Strength of the repulsion force.

                             nudge_x = 0,
                             # Do not repel from top or bottom edges.
                             ylim = c(1, Inf),
                             direction    = "y",
                             angle        = 90,
                             hjust        = 0,
                             segment.size = 1/20,    ## segment width
                             segment.linewidth = 1/12,#0.01,
                             arrow = arrow(length = unit(0.04, 'npc')),     # Draw an arrow from the label to the data point.
                             
                             
                             max.overlaps = 50,
                             max.iter = 3e3,     # Maximum iterations of the naive repulsion algorithm O(n^2).
                             color = "grey10"
  ) +
  scale_y_continuous(limits=c(-1.5,8.5),expand = c(0,0)) +
  scale_color_manual(values = patient_kclust3_lab_conv) +
      coord_cartesian(clip = "off") +

  #coord_flip() +
  
  labs(x="Severity associated proteins in plasma",
       y="NPX",
       color=NULL,
       caption = "meanNPX +- ci95") +
  theme(legend.position = "top",
        axis.text.x = element_text(colour = "black",angle=90,hjust=1,vjust=.5,size = 2),
        axis.text.y = element_text(size = 6),
        panel.grid.minor = element_line(size = 0.1),
        panel.grid.major = element_line(size = .1),
        #axis.text.x = element_blank()
        )
)

require(patchwork)
(p_annotation <- #secretome_location_dap_severity%>% 
    #transmute(Assay, secretome_location_tissue_spec) %>% 
   # left_join(tmp.df,by="Assay") %>% 
    tmp.df %>% 
    mutate(dummy.y = "HPA") %>% 
    ggplot(aes(x = fct_reorder(Assay,NPXmean,.desc = F), y = dummy.y, fill = secretome_location_tissue_spec)) +
    geom_tile(linejoin = "round") +
    scale_fill_manual(values = secretome_location_tissue_spec_cols) +
    theme_void() +
    theme(legend.position = "none") 
  #scale_y_discrete(expand=c(0,-0.1))
   # theme(aspect.ratio = 1/100)
  )

test_plot <- p_annotation / turqoise_allProteins_lab + plot_layout(height = c(.5, 4))
test_plot

Figure 7D

## create a gene name - uniprot dictionary
name_up_dict <- hpa_24.0 %>% transmute(gene, uniprot)

ligand.q <- dap.res %>% filter(p.adj <=0.01, logFC > .1) %>% 
  left_join(cpdb.protein_input,
            by=c("UniProt"="uniprot")) #%>% 
  #pull(UniProt)

length(ligand.q)

## [1] 32

interaction_dict <- cpdb.interaction_input %>% 
  filter(partner_a %in% ligand.q$UniProt,
         directionality == "Ligand-Receptor"
        #directionality %in% c("Ligand-Receptor","Receptor-Receptor","Ligand-Ligand")
         ) %>% 
  mutate(protein_name_b_strip = gsub("_HUMAN","",protein_name_b),
         protein_name_a = gsub("_HUMAN","",protein_name_a)) %>% 
  mutate(protein_name_b_complex = case_when(is.na(protein_name_b) ~ str_remove(interactors,paste0(protein_name_a,"-")),
                                    .default = protein_name_b)) %>%
   separate_longer_delim(protein_name_b_complex, delim = "+") %>% 
   left_join(hpa_24.0 %>% transmute(protein_name_b_complex = gene,
                                      uniprot_b_complex = uniprot), by=c("protein_name_b_complex")) %>% 
  mutate(protein_name_b = case_when(is.na(protein_name_b) ~ protein_name_b_complex,
                                        .default = protein_name_b),
         partner_b_new = case_when(is.na(uniprot_b_complex) ~ partner_b,
                                   .default = uniprot_b_complex)) %>% 
  transmute(partner_a, partner_b, partner_b_new) %>% 
  mutate(uniprot_a = partner_a,
         uniprot_b = partner_b_new) %>% 
  transmute(source = uniprot_a,
            recipient = uniprot_b) %>% 
  left_join(name_up_dict %>% dplyr::rename(source_gene = gene), by=c("source" = "uniprot")) %>% 
  left_join(name_up_dict %>% dplyr::rename(recipient_gene = gene), by=c("recipient" = "uniprot"))
interaction_dict

## # A tibble: 262 × 4
##    source recipient source_gene recipient_gene
##    <chr>  <chr>     <chr>       <chr>         
##  1 P19022 P06734    CDH2        FCER2         
##  2 P05362 P20701    ICAM1       ITGAL         
##  3 P05362 P20701    ICAM1       ITGAL         
##  4 P05362 P05107    ICAM1       ITGB2         
##  5 P05362 P11215    ICAM1       ITGAM         
##  6 P05362 P05107    ICAM1       ITGB2         
##  7 P05362 P20702    ICAM1       ITGAX         
##  8 P05362 P05107    ICAM1       ITGB2         
##  9 P13598 Q9NNX6    ICAM2       CD209         
## 10 P13598 P20701    ICAM2       ITGAL         
## # ℹ 252 more rows

celltype_l2_freq <- tibble(pbmc_acute@meta.data) %>% 
  group_by(CellType_L2) %>% 
  summarise(n = n()) %>%
  mutate(freq = n / sum(n),
         Percentage = freq*100) 

celltype_l2_of_l1_freq <- tibble(pbmc_acute@meta.data) %>% 
  group_by(CellType_L1,CellType_L2) %>% 
  summarise(n = n()) %>%
  group_by(CellType_L1) %>% 
  mutate(freq = n / sum(n),
         Percentage = freq*100) 

circosplot function

my_nice_circosplot <- function(assays2plot_circos, scale_range, expression_threshold, pdf_file_name){
  
pbmc_acute.avg.long_tourquoise <- pbmc_acute.avg.long %>% 
  filter(celltype != "undefined",
         gene %in% assays2plot_circos,
         ) %>% 
  mutate(gene_ct = paste0(gene,"_",celltype)) %>% 
  group_by(gene) %>% 
  mutate(avgExp = scales::rescale(avgExp, to=scale_range)) %>%  #c(0,1)
  ungroup() 

mat <- pbmc_acute.avg.long_tourquoise %>% 
    filter(avgExp >expression_threshold) %>% #.5
  left_join(tibble(pbmc@meta.data) %>% transmute(celltype_1 = CellType_L1,
                                                celltype = CellType_L2) %>% distinct(), by="celltype") %>% 
  mutate(celltype_1 = factor(celltype_1, levels= c("DC","Monocytes","NK","gdT","B","CD4+ T","CD8+ T")),
         celltype = factor(celltype, levels = c("mDC", "pDC", 
                                                "CD14 monocytes", "CD16 monocytes",
                                                "NK CD56dim CD16+", "NK CD56dim","NK CD56bright","NK prolif.",
                                                "Vd2+ gdT", "Vd2- gdT",
                                                "B naive", "B memory", "Plasma cells",
                                                "CD4 naive", "CD4 Treg CD80+", "CD4 Treg CD80-", "CD4 Tfh",
                                                "CD4 effect. activated", "CD4 effect. memory",
                                                "CD4 trans. memory","CD4 central memory",
                                                "CD8 naive", "CD8 trans. memory", "CD8 Tfh",
                                                "NKT", "CD8 effect. memory"))) %>% 
  add_rownames() 


tmp <- mat %>% dplyr::rename(index = rowname) 

df_link <- interaction_dict %>% 
  transmute(source_gene, recipient_gene) %>% 
  left_join(tmp %>% 
               filter(gene %in% interaction_dict$source_gene) %>%
               transmute(from_index = index,
                         gene), 
             by=c("source_gene"="gene")) %>% 
  filter(!is.na(from_index)) %>% 
  left_join(tmp %>% 
               transmute(to_index = index,
                         gene), 
             by=c("recipient_gene"="gene")) %>% 
  filter(!is.na(to_index)) %>% 
  distinct() %>% 
  right_join(mat %>% transmute(gene, celltype) %>% 
               left_join(data.frame(celltype = names(L2_colors), 
                                    source_celltype_colors = L2_colors)),
              by=c("source_gene"="gene")) %>% 
  
  transmute(from_index = as.integer(from_index),
            to_index = as.integer(to_index),
            source_celltype = celltype,
            source_gene,
            recipient_gene) %>% 
  na.omit() %>% 
  distinct()

## goal
## from_index; to_index data frame


mat_gex <- mat %>% arrange(celltype) %>%
  column_to_rownames("gene_ct") %>% 
  dplyr::select(avgExp)

mat_npx <- mat %>%
  transmute(gene_ct, gene) %>% 
  left_join(df_acute_patclust_incl_conv %>% 
              transmute(Assay, NPX,severity_lab) %>% 
              #filter(Assay %in% restricted_module_turquoise) %>% 
              pivot_wider(names_from = severity_lab, values_from = NPX,values_fn = median)
            , by=c("gene"="Assay")) %>% 
  dplyr::select(-gene) %>% 
  distinct() %>%
  column_to_rownames("gene_ct") %>%
  relocate(severe, moderate, mild, convalescence)


## legends
col_npx <- colorRamp2(c(min(mat_npx,na.rm = T),
                        0,
                        max(mat_npx,na.rm = T)/2,
                        max(mat_npx,na.rm = T)),
                      c("#edf8e9","#bae4b3", "#74c476","#238b45"))

#mat_npx <- mat_npx %>% mutate(across(where(is.numeric), ~ scales::rescale(., to=c(4,0))))
cell_freq_color <- colorRamp2(c(0,
                                min(celltype_l2_freq$Percentage,na.rm = T),
                                mean(celltype_l2_freq$Percentage,na.rm=T),
                                max(celltype_l2_freq$Percentage,na.rm = T)),
                              c("#f2f0f7","#cbc9e2","#9e9ac8","#6a51a3"))

lgd_npx = Legend(title = "NPX", col_fun = col_npx,
                 title_gp = gpar(fontsize=6,fontface="bold"),
                      labels_gp = gpar(fontsize=6))

lgd_gex = Legend(title = "GEX", col_fun = scaled_01_col,
                 title_gp = gpar(fontsize=6,fontface="bold"),
                      labels_gp = gpar(fontsize=6))

lgd_celltype_freq = Legend(title = "Cell frequency\nof CD45+",
                           col_fun = cell_freq_color,
                 title_gp = gpar(fontsize=6,fontface="bold"),
                      labels_gp = gpar(fontsize=6))

lgd_severity = Legend(title = "Severity group", 
                      at = c("severe","moderate","mild","convalescence"),
                      legend_gp = gpar(fill = c("#ca0020","#f4a582","#92c5de","grey50")),
                      title_gp = gpar(fontsize=6,fontface="bold"),
                      labels_gp = gpar(fontsize=6))


lgd_celltype = Legend(title = "Celltypes", 
                      at = c("DC","Monocytes","NK","gdT","B","CD4+ T","CD8+ T"),
                      legend_gp = gpar(fill = c("#ca5369","#688bcc","#8761cc", "#ae953e",
                                                "#c361aa","#68a748","#cc693d")),
                      ncol = 1,
                      #nrow = 1,
                      title_gp = gpar(fontsize=6,fontface="bold"),
                      labels_gp = gpar(fontsize=6))

lgd_celltype_2 = Legend(title = "Celltypes", 
                      at = c("mDC","pDC",
                             "CD14 monocytes","CD16 monocytes",
                             "NK CD56dim CD16+","NK CD56dim","NKCD56bright","NK prolif.","NKT",
                             "Vd2+ gdT","Vd2- gdT",
                             "B naive",
                             "B memory",
                             "Plasma cells",
                             "CD4 naive", "CD4 Treg CD80+", "CD4 Treg CD80-", "CD4 Tfh",
                             "CD4 effect. activated","CD4 effect. memory","CD4 trans.memory","CD central memory",
                             "CD8 naive", "CD8 trans. memory","CD8Tfh","CD8 effect. memory"),
                             #,(L2_colors),
                      legend_gp = gpar(fill = L2_colors),
                      
                      ncol=1,
                      #nrow = 4,
                      title_gp = gpar(fontsize=6,fontface="bold"),
                      labels_gp = gpar(fontsize=6))

circle_size = unit(1, "snpc") # snpc unit gives you a square region

## == circos.heatmap.get.x start ====

## A function to extract row indicies, useful for labelling

## source: https://rdrr.io/github/jokergoo/circlize/src/R/circos.heatmap.R
# == title
# Get the x-position for heatmap rows
#
# == param
# -row_ind A vector of row indicies.
#
# == value
# A three-column data frame of the sector, the x-positions on the corresponding sectors, and the original row indicies.
circos.heatmap.get.x = function(row_ind) {
    env = circos.par("__tempenv__")
    split = env$circos.heatmap.split

    row_ind_lt = split(row_ind, split[row_ind])
    row_ind_lt = row_ind_lt[sapply(row_ind_lt, length) > 0]
    
    x = NULL
    for(i in row_ind_lt) {

        subset = get.cell.meta.data("subset", sector.index = split[i[1]])
        order = get.cell.meta.data("row_order", sector.index = split[i[1]])
        
        x = c(x, which((1:length(split))[subset][order] %in% i))
    }
    df = data.frame(sector = rep(names(row_ind_lt), times = sapply(row_ind_lt, length)), 
        x = x - 0.5, row_ind = unlist(row_ind_lt))
    rownames(df) = NULL
    df
}
## == circos.heatmap.get.x end ====

total_sections <- length(levels(mat$celltype))


## the function to make the plot
circlize_plot = function() {
    circos.clear()

  circos.par(gap.after = c(rep(2,total_sections-1),10), 
             points.overflow.warning = T)
#circos.par(start.degree = 90, gap.degree = 10,gap.after = c(3))

## dummy track, invisible, needed for split
circos.heatmap(mat_gex,
               cluster = F,
               split = droplevels(mat$celltype),
               col = colorRamp2(c(-2, 0, 2), c("white", "white", "white")), 
               track.height = 0.21,#0.000000001,
               )

## celltype annotation track
circos.heatmap(mat %>% column_to_rownames("gene_ct") %>% dplyr::select(celltype), 
               col = L2_colors, 
               track.height = 0.08,
               rownames.side = "none",
 )

## celltype frequency track
circos.heatmap(mat %>% column_to_rownames("gene_ct") %>% transmute(CellType_L2 = celltype) %>% left_join(celltype_l2_freq, by="CellType_L2") %>% pull(Percentage), col = cell_freq_color, track.height = 0.01)

## celltype annotation tack naming
circos.trackPlotRegion(track.index = 1, panel.fun = function(x, y) {
  xlim = get.cell.meta.data("xlim")
  ylim = get.cell.meta.data("ylim")
  sector.name = get.cell.meta.data("sector.index")
  circos.text(mean(xlim),
              ylim[1] + .1, 
              sector.name, 
              facing = "clockwise", 
              niceFacing = TRUE, cex=.6,
              adj = c(0, 0.5), col = "grey40")
}, bg.border = NA)

## celltype gene expression track
circos.heatmap(mat_gex,
               cluster = F, 
               col = scaled_01_col, 
               track.height = 0.04,
               # rownames.side = "outside",
               bg.border = "grey80", 
               bg.lwd = .1,
               bg.lty = .1, 
               show.sector.labels = F
)

## plasma NPX trac
circos.heatmap(mat_npx, col = col_npx, track.height = 0.09)

## add annotation to row of npx data
circos.track(track.index = get.current.track.index(), panel.fun = function(x, y) {
    if(CELL_META$sector.numeric.index == total_sections) { # the last sector #26
      ## conval
        circos.rect(CELL_META$cell.xlim[2] + convert_x(1, "mm"), 0,
                    CELL_META$cell.xlim[2] + convert_x(4, "mm"), 1, #10
                    col = "grey50", border = NA)
      ## mild  
      circos.rect(CELL_META$cell.xlim[2] + convert_x(1, "mm"), 1,
                    CELL_META$cell.xlim[2] + convert_x(4, "mm"), 2, #5
                    col = "#92c5de", border = NA)
      ## moderate
        circos.rect(CELL_META$cell.xlim[2] + convert_x(1, "mm"), 2,
                    CELL_META$cell.xlim[2] + convert_x(4, "mm"), 3, #10
                    col = "#f4a582", border = NA)
        ## severe
        circos.rect(CELL_META$cell.xlim[2] + convert_x(1, "mm"), 3,
                    CELL_META$cell.xlim[2] + convert_x(4, "mm"), 4, #10
                    col = "#ca0020", border = NA)
       
    }
}, bg.border = NA)

## Annotate source genes
row_ind <- mat %>% filter(gene%in%df_link$source_gene) %>% mutate(rowname = as.integer(rowname)) %>% pull(rowname)
pos_so = circos.heatmap.get.x(row_ind)
pos_so <- pos_so %>% right_join(mat %>% filter(gene%in%df_link$source_gene) %>% mutate(row_ind = as.integer(rowname)), by="row_ind")

## Annotate recipient genes
row_ind <- mat %>% filter(gene%in%df_link$recipient_gene) %>% mutate(rowname = as.integer(rowname)) %>% pull(rowname)
pos_rec = circos.heatmap.get.x(row_ind)
pos_rec <- pos_rec %>% right_join(mat %>% filter(gene%in%df_link$recipient_gene) %>% mutate(row_ind = as.integer(rowname)), by="row_ind")

pos <- bind_rows(pos_so, pos_rec)

## lable all other genes

## Annotate source genes
row_ind_allothers <- mat %>% filter(!gene %in% c(df_link$source_gene,df_link$recipient_gene)) %>% mutate(rowname = as.integer(rowname)) %>% pull(rowname)

pos_allothers = circos.heatmap.get.x(row_ind_allothers) %>% 
  left_join(mat %>% mutate(row_ind = as.integer(rowname)), by="row_ind")

## join all lable info
pos_all <- bind_rows(pos %>% mutate(col = "black",
                                    size = .4),
                     pos_allothers %>% mutate(col = "grey",
                                              size=.2))

circos.labels(pos_all$sector, 
              pos_all$x,
              connection_height =.01,
              cex =pos_all$size,
              side="inside",
              col = pos_all$col, 
              labels = pos_all$gene)

## add connections
for(i in seq_len(nrow(df_link))) {

        circos.heatmap.link(df_link$from_index[i],
                        df_link$to_index[i],
                        col = rand_color(1),
                        
                        lwd = 1.5,
                        directional = 1,
                        arr.width = .125,
                        arr.length = .2,
                        arr.lwd = .1,
                       arr.col = "black")
}


  circos.clear()
}

library(gridBase)
pdf(paste0(result.tmp.dir,pdf_file_name,".pdf"))#,paper = "a4r")
plot.new()

circle_size = unit(1, "snpc") # snpc unit gives you a square region

pushViewport(viewport(x = 0.5, y = 1,#0.5,
                      width = circle_size, 
                      height = circle_size,
    just =  c("center", "top")))
par(omi = gridOMI(), new = TRUE)
circlize_plot()
upViewport()

draw(packLegend(lgd_gex, lgd_npx,
                direction = "horizontal"),
     y = unit(1, "npc") - circle_size*.1, 
     x = unit(1.04,"npc") - circle_size*0.1,
     just = c("center","right"))

draw(packLegend(lgd_celltype_freq,
                direction = "horizontal"),
     #y = unit(1, "npc") - circle_size*.1, 
     x = unit(1.04,"npc") - circle_size*0.1,
     just = c("center","right"))


draw(packLegend(lgd_severity,
                direction = "horizontal"),
     y = unit(1, "npc") - circle_size*.8, 
     x = unit(1.0,"npc") - circle_size*0.11,
     just = c("bottom","left"))
dev.off()
return(circlize_plot())
}

my_nice_circosplot(assays2plot_circos = restricted_module_turquoise,
                   scale_range = c(0,1),
                   expression_threshold = 0.5,
                   pdf_file_name = "ImmuneCell_Protein_CircosPlot_severitymodule"
                   )

Figure 7E

my_comparisons_severe_conv <- list(c("severe", "moderate"), c("moderate", "mild"), c("severe", "mild"),c("mild","convalescence"))

selection <- c("LGALS9","IL4","CD274","CD70")

(severity_ligand_npx <- df_acute_patclust_incl_conv %>% 

    dplyr::filter(Assay %in% c(selection)) %>% 
    mutate(Assay = factor(Assay, levels = c(selection))) %>% 
    ggplot(aes(x=severity_lab, y=NPX, color=severity_lab, fill=severity_lab)) + 
    geom_violin(trim = F,alpha=.9) +
    geom_jitter(size=0.25,show.legend = F, width = 0.05, alpha=1, color="grey20") +
    geom_boxplot(alpha=.7,width=0.25,outlier.shape = NA,color="black", fatten = 2,lwd=.25,show.legend = F) +
    stat_compare_means(method = "wilcox.test",
                       label.sep = "\n",
                       hide.ns = T,
                       label = "p.signif" ,
                       vjust = .5,
                       size=2,
                       lwd = .2,
                       comparisons =my_comparisons_severe_conv,
                       show.legend = F) +
    facet_wrap(~Assay,nrow = 2,scales = "free_y") +
    theme_minimal() +
    theme(legend.position="bottom",
          axis.text.x = element_blank()) +
    labs(x="",
         color=NULL,
         fill=NULL) +
    scale_color_manual(values= patient_kclust3_lab_conv) +
    scale_fill_manual(values= patient_kclust3_lab_conv))

Figure 7F

#FACs_data %>% distinct(feature)

cellsubset.order <- FACs_data %>% 
  filter(feature%in%c("CD4+CD38+HLADR+ T cells","CD8+CD38+HLADR+ T cells"),
#    grepl("Treg",feature)
    ) %>% distinct(feature) %>% pull()

test_correlation_input <- FACs_data %>% 
  filter(Time=="Acute",
         feature%in%
           c(
           "CD4+CD38+HLADR+ T cells",
           "CD8+CD38+HLADR+ T cells"
         )
  ) %>% 
  transmute(sample_id = sampleID,
            type_feature = paste0("FACS_",feature),
            value) %>% 
  pivot_wider(values_from = value, names_from = type_feature) %>% 
  inner_join(
    ## Plasma protein data from this paper
    data.long %>% 
      inner_join(sampleTable_simple) %>% 
      filter(Assay %in% restricted_module_turquoise) %>% 
      transmute(
        sample_id,
        type_assay = paste0("PEA_",Assay),
        NPX) %>% 
      pivot_wider(values_from = NPX, names_from = type_assay),
    by="sample_id")

test_correlation_res <- test_correlation_input %>% 
  column_to_rownames("sample_id") %>% 
  correlation(p_adjust = "fdr",method = "spearman",redundant = F) %>% 
  tibble()

cor.g <- test_correlation_res %>% 
  filter(Parameter1!=Parameter2) %>% 
  filter(
    !grepl("PEA",Parameter1),
    !grepl("FACS",Parameter2)
  ) %>% 
   arrange(-abs(rho)) %>% 
  filter(p<=0.05) %>% 
     transmute(from = Parameter1,# = str_remove(Parameter1, "FACS_"),
            to = Parameter2,# = str_remove(Parameter2, "PEA_"),
            rho,
            p
            ) %>% 
  as_tbl_graph(directed = F)

node_table <- as_tibble(cor.g) %>% 
  separate(name, into=c("omics","feature"),sep = "_",remove = F) 

(protein_cellnum_cornet <- cor.g %>% 
  inner_join(node_table,by="name") %>% 
    activate(nodes) %>%  # Sets context to nodes -> subsequent operations are performed on nodes
  mutate(deg = centrality_degree()) %>% 
  filter(!node_is_isolated()) %>%  # Removes nodes that are isolated/do not have any follower edges
# create_layout(layout = "igraph", algorithm = "fr") %>% 
  create_layout(layout = "stress") %>%  #fr
  ggraph() +
    geom_edge_link(aes(color = rho),
                   #    alpha = 0.9
                   ) +  
  scale_edge_color_continuous(low="thistle2",
                              high="darkred") +
  geom_node_point(aes(color = omics,
                      size= ifelse(omics=="FACS",3,1)),
                  show.legend = F) +
  geom_node_text(aes(label = feature,
                     alpha= ifelse(deg>1,1,.5)
                     ),
                 color="black",
                 size=1.5,
                 repel = T,show.legend = F
                     ) +
  scale_alpha_continuous(range = c(0.5, 1)) +
  theme_void() +
    guides(color= guide_colorbar(barheight = 1, barwidth = .1)) +

   theme(legend.position = "right",
         plot.title = element_text(size=6),
         legend.title = element_text( size=6),
         legend.text=element_text(size=6)) 

)

Session Info

sessionInfo()

## R version 4.3.2 (2023-10-31)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Sonoma 14.7.4
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: Europe/Stockholm
## tzcode source: internal
## 
## attached base packages:
## [1] grid      stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] gridBase_0.4-7        GSVA_1.48.3           UpSetR_1.4.0         
##  [4] see_0.8.0             pathview_1.40.0       ggtext_0.1.2         
##  [7] gtsummary_1.7.2       emmeans_1.8.7         lmerTest_3.1-3       
## [10] lme4_1.1-34           eulerr_7.0.2          mixOmics_6.24.0      
## [13] lattice_0.21-8        MASS_7.3-60           WGCNA_1.72-1         
## [16] fastcluster_1.2.3     dynamicTreeCut_1.63-1 scales_1.2.1         
## [19] ggraph_2.1.0          tidygraph_1.2.3       umap_0.2.10.0        
## [22] clusterProfiler_4.8.2 SeuratObject_4.1.3    Seurat_4.3.0.1       
## [25] ggalluvial_0.12.5     ggrepel_0.9.3         correlation_0.8.4    
## [28] ggpubr_0.6.0          igraph_1.5.0.1        broom_1.0.5          
## [31] circlize_0.4.15       ComplexHeatmap_2.16.0 RColorBrewer_1.1-3   
## [34] viridis_0.6.4         viridisLite_0.4.2     gridExtra_2.3        
## [37] patchwork_1.1.2       Matrix_1.6-0          DT_0.28              
## [40] readxl_1.4.3          lubridate_1.9.2       forcats_1.0.0        
## [43] stringr_1.5.0         dplyr_1.1.2           purrr_1.0.1          
## [46] readr_2.1.4           tidyr_1.3.0           tibble_3.2.1         
## [49] ggplot2_3.4.2         tidyverse_2.0.0      
## 
## loaded via a namespace (and not attached):
##   [1] graph_1.78.0                ica_1.0-3                  
##   [3] plotly_4.10.2               Formula_1.2-5              
##   [5] zlibbioc_1.46.0             tidyselect_1.2.0           
##   [7] bit_4.0.5                   doParallel_1.0.17          
##   [9] clue_0.3-64                 rjson_0.2.21               
##  [11] blob_1.2.4                  broom.helpers_1.13.0       
##  [13] S4Arrays_1.0.5              pbkrtest_0.5.2             
##  [15] parallel_4.3.2              Biobase_2.60.0             
##  [17] png_0.1-8                   cli_3.6.3                  
##  [19] ggplotify_0.1.1             bayestestR_0.13.1          
##  [21] askpass_1.1                 openssl_2.1.0              
##  [23] goftest_1.2-3               broom.mixed_0.2.9.4        
##  [25] uwot_0.1.16                 shadowtext_0.1.2           
##  [27] curl_5.0.1                  mime_0.12                  
##  [29] evaluate_0.21               tidytree_0.4.4             
##  [31] leiden_0.4.3                V8_4.3.3                   
##  [33] stringi_1.7.12              backports_1.4.1            
##  [35] XML_3.99-0.14               httpuv_1.6.11              
##  [37] AnnotationDbi_1.62.2        magrittr_2.0.3             
##  [39] splines_4.3.2               org.Hs.eg.db_3.17.0        
##  [41] sctransform_0.3.5           ggbeeswarm_0.7.2           
##  [43] DBI_1.1.3                   ggExtra_0.10.1             
##  [45] HDF5Array_1.28.1            jquerylib_0.1.4            
##  [47] withr_2.5.0                 corpcor_1.6.10             
##  [49] enrichplot_1.20.0           lmtest_0.9-40              
##  [51] GSEABase_1.62.0             htmlwidgets_1.6.2          
##  [53] S4Vectors_0.38.1            SingleCellExperiment_1.22.0
##  [55] ggvenn_0.1.10               labeling_0.4.2             
##  [57] cellranger_1.1.0            MatrixGenerics_1.12.3      
##  [59] annotate_1.78.0             reticulate_1.30            
##  [61] zoo_1.8-12                  XVector_0.40.0             
##  [63] knitr_1.43                  BiocGenerics_0.46.0        
##  [65] gt_0.9.0                    timechange_0.2.0           
##  [67] foreach_1.5.2               fansi_1.0.4                
##  [69] data.table_1.14.8           ggtree_3.8.0               
##  [71] rhdf5_2.44.0                RSpectra_0.16-1            
##  [73] irlba_2.3.5.1               ggrastr_1.0.2              
##  [75] gridGraphics_0.5-1          commonmark_1.9.0           
##  [77] ellipsis_0.3.2              lazyeval_0.2.2             
##  [79] yaml_2.3.7                  survival_3.5-7             
##  [81] scattermore_1.2             crayon_1.5.2               
##  [83] RcppAnnoy_0.0.21            progressr_0.13.0           
##  [85] tweenr_2.0.2                later_1.3.1                
##  [87] Rgraphviz_2.44.0            ggridges_0.5.4             
##  [89] codetools_0.2-19            base64enc_0.1-3            
##  [91] GlobalOptions_0.1.2         KEGGREST_1.40.0            
##  [93] ggfittext_0.10.1            Rtsne_0.16                 
##  [95] shape_1.4.6                 estimability_1.4.1         
##  [97] foreign_0.8-85              pkgconfig_2.0.3            
##  [99] KEGGgraph_1.60.0            xml2_1.3.5                 
## [101] GenomicRanges_1.52.0        IRanges_2.34.1             
## [103] aplot_0.1.10                spatstat.sparse_3.0-2      
## [105] ape_5.7-1                   xtable_1.8-4               
## [107] car_3.1-2                   highr_0.10                 
## [109] plyr_1.8.8                  polylabelr_0.2.0           
## [111] httr_1.4.6                  tools_4.3.2                
## [113] globals_0.16.2              beeswarm_0.4.0             
## [115] htmlTable_2.4.1             checkmate_2.2.0            
## [117] nlme_3.1-163                HDO.db_0.99.1              
## [119] digest_0.6.33               numDeriv_2016.8-1.1        
## [121] furrr_0.3.1                 farver_2.1.1               
## [123] tzdb_0.4.0                  reshape2_1.4.4             
## [125] yulab.utils_0.0.6           rpart_4.1.21               
## [127] glue_1.6.2                  cachem_1.0.8               
## [129] polyclip_1.10-4             Hmisc_5.1-0                
## [131] generics_0.1.3              Biostrings_2.68.1          
## [133] stats4_4.3.2                mvtnorm_1.2-2              
## [135] parallelly_1.36.0           impute_1.74.1              
## [137] ScaledMatrix_1.8.1          carData_3.0-5              
## [139] minqa_1.2.5                 pbapply_1.7-2              
## [141] randomcoloR_1.1.0.1         SummarizedExperiment_1.30.2
## [143] vroom_1.6.3                 gson_0.1.0                 
## [145] utf8_1.2.3                  graphlayouts_1.0.0         
## [147] datawizard_0.8.0            preprocessCore_1.62.1      
## [149] ggsignif_0.6.4              shiny_1.7.4.1              
## [151] GenomeInfoDbData_1.2.10     rhdf5filters_1.12.1        
## [153] parameters_0.21.1           RCurl_1.98-1.12            
## [155] memoise_2.0.1               rmarkdown_2.23             
## [157] downloader_0.4              future_1.33.0              
## [159] RANN_2.6.1                  Cairo_1.6-1                
## [161] spatstat.data_3.0-1         rstudioapi_0.15.0          
## [163] cluster_2.1.4               janitor_2.2.0              
## [165] spatstat.utils_3.0-3        hms_1.1.3                  
## [167] fitdistrplus_1.1-11         munsell_0.5.0              
## [169] cowplot_1.1.1               colorspace_2.1-0           
## [171] ellipse_0.5.0               rlang_1.1.1                
## [173] GenomeInfoDb_1.36.1         DelayedMatrixStats_1.22.6  
## [175] sparseMatrixStats_1.12.2    ggforce_0.4.1              
## [177] mgcv_1.9-0                  xfun_0.39                  
## [179] coda_0.19-4                 iterators_1.0.14           
## [181] matrixStats_1.0.0           rARPACK_0.11-0             
## [183] abind_1.4-5                 GOSemSim_2.26.1            
## [185] treeio_1.25.2               Rhdf5lib_1.22.1            
## [187] bitops_1.0-7                promises_1.2.0.1           
## [189] scatterpie_0.2.1            RSQLite_2.3.1              
## [191] qvalue_2.32.0               fgsea_1.26.0               
## [193] DelayedArray_0.26.7         GO.db_3.17.0               
## [195] compiler_4.3.2              beachmat_2.16.0            
## [197] boot_1.3-28.1               listenv_0.9.0              
## [199] Rcpp_1.0.11                 BiocSingular_1.16.0        
## [201] tensor_1.5                  BiocParallel_1.34.2        
## [203] insight_0.19.3              gridtext_0.1.5             
## [205] spatstat.random_3.1-5       R6_2.5.1                   
## [207] fastmap_1.1.1               fastmatch_1.1-3            
## [209] rstatix_0.7.2               vipor_0.4.5                
## [211] ROCR_1.0-11                 rsvd_1.0.5                 
## [213] nnet_7.3-19                 gtable_0.3.3               
## [215] KernSmooth_2.23-22          miniUI_0.1.1.1             
## [217] deldir_1.0-9                htmltools_0.5.5            
## [219] bit64_4.0.5                 spatstat.explore_3.2-1     
## [221] lifecycle_1.0.3             nloptr_2.0.3               
## [223] sass_0.4.7                  vctrs_0.6.3                
## [225] spatstat.geom_3.2-4         snakecase_0.11.0           
## [227] DOSE_3.26.1                 ggfun_0.1.1                
## [229] sp_2.0-0                    future.apply_1.11.0        
## [231] bslib_0.5.0                 pillar_1.9.0               
## [233] magick_2.8.1                jsonlite_1.8.7             
## [235] markdown_1.7                GetoptLong_1.0.5

Figure Panels

source_rmd <- function(rmd_file){
  knitr::knit(rmd_file, output = tempfile())
}

source_rmd("Make_my_figurepanels.Rmd")

## make one Pdf
library(qpdf)
qpdf::pdf_combine(
  input = c("../Manuscript/Figure_1.pdf", 
            "../Manuscript/Figure_2.pdf",
            "../Manuscript/Figure_3.pdf", 
            "../Manuscript/Figure_4.pdf", 
            "../Manuscript/Figure_5.pdf", 
            "../Manuscript/Figure_6.pdf",
            "../Manuscript/Figure_7.pdf"),
  output = "../Manuscript/Lautenbach_etal_mainfigures.pdf"
)

qpdf::pdf_combine(
  input = c("../Manuscript/Figure_1_S1.pdf", 
            "../Manuscript/Figure_1_S2.pdf", 
            "../Manuscript/Figure_1_S3.pdf", 
            
            "../Manuscript/Figure_2_S4.pdf",
            "../Manuscript/Figure_2_S5.pdf", 
            
            "../Manuscript/Figure_3_S6.pdf", 
            "../Manuscript/Figure_3_S7.pdf", 
            
            "../Manuscript/Figure_4_S8.pdf",
            
            "../Manuscript/Figure_5_S9.pdf"
            ),
  output = "../Manuscript/Lautenbach_etal_supplementaryfigures.pdf"
)

sessionInfo()

## R version 4.3.2 (2023-10-31)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Sonoma 14.7.4
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## time zone: Europe/Stockholm
## tzcode source: internal
## 
## attached base packages:
## [1] grid      stats     graphics  grDevices utils     datasets  methods  
## [8] base     
## 
## other attached packages:
##  [1] gridBase_0.4-7        GSVA_1.48.3           UpSetR_1.4.0         
##  [4] see_0.8.0             pathview_1.40.0       ggtext_0.1.2         
##  [7] gtsummary_1.7.2       emmeans_1.8.7         lmerTest_3.1-3       
## [10] lme4_1.1-34           eulerr_7.0.2          mixOmics_6.24.0      
## [13] lattice_0.21-8        MASS_7.3-60           WGCNA_1.72-1         
## [16] fastcluster_1.2.3     dynamicTreeCut_1.63-1 scales_1.2.1         
## [19] ggraph_2.1.0          tidygraph_1.2.3       umap_0.2.10.0        
## [22] clusterProfiler_4.8.2 SeuratObject_4.1.3    Seurat_4.3.0.1       
## [25] ggalluvial_0.12.5     ggrepel_0.9.3         correlation_0.8.4    
## [28] ggpubr_0.6.0          igraph_1.5.0.1        broom_1.0.5          
## [31] circlize_0.4.15       ComplexHeatmap_2.16.0 RColorBrewer_1.1-3   
## [34] viridis_0.6.4         viridisLite_0.4.2     gridExtra_2.3        
## [37] patchwork_1.1.2       Matrix_1.6-0          DT_0.28              
## [40] readxl_1.4.3          lubridate_1.9.2       forcats_1.0.0        
## [43] stringr_1.5.0         dplyr_1.1.2           purrr_1.0.1          
## [46] readr_2.1.4           tidyr_1.3.0           tibble_3.2.1         
## [49] ggplot2_3.4.2         tidyverse_2.0.0      
## 
## loaded via a namespace (and not attached):
##   [1] graph_1.78.0                ica_1.0-3                  
##   [3] plotly_4.10.2               Formula_1.2-5              
##   [5] zlibbioc_1.46.0             tidyselect_1.2.0           
##   [7] bit_4.0.5                   doParallel_1.0.17          
##   [9] clue_0.3-64                 rjson_0.2.21               
##  [11] blob_1.2.4                  broom.helpers_1.13.0       
##  [13] S4Arrays_1.0.5              pbkrtest_0.5.2             
##  [15] parallel_4.3.2              Biobase_2.60.0             
##  [17] png_0.1-8                   cli_3.6.3                  
##  [19] ggplotify_0.1.1             bayestestR_0.13.1          
##  [21] askpass_1.1                 openssl_2.1.0              
##  [23] goftest_1.2-3               broom.mixed_0.2.9.4        
##  [25] uwot_0.1.16                 shadowtext_0.1.2           
##  [27] curl_5.0.1                  mime_0.12                  
##  [29] evaluate_0.21               tidytree_0.4.4             
##  [31] leiden_0.4.3                V8_4.3.3                   
##  [33] stringi_1.7.12              backports_1.4.1            
##  [35] XML_3.99-0.14               httpuv_1.6.11              
##  [37] AnnotationDbi_1.62.2        magrittr_2.0.3             
##  [39] splines_4.3.2               org.Hs.eg.db_3.17.0        
##  [41] sctransform_0.3.5           ggbeeswarm_0.7.2           
##  [43] DBI_1.1.3                   ggExtra_0.10.1             
##  [45] HDF5Array_1.28.1            jquerylib_0.1.4            
##  [47] withr_2.5.0                 corpcor_1.6.10             
##  [49] enrichplot_1.20.0           lmtest_0.9-40              
##  [51] GSEABase_1.62.0             htmlwidgets_1.6.2          
##  [53] S4Vectors_0.38.1            SingleCellExperiment_1.22.0
##  [55] ggvenn_0.1.10               labeling_0.4.2             
##  [57] cellranger_1.1.0            MatrixGenerics_1.12.3      
##  [59] annotate_1.78.0             reticulate_1.30            
##  [61] zoo_1.8-12                  XVector_0.40.0             
##  [63] knitr_1.43                  BiocGenerics_0.46.0        
##  [65] gt_0.9.0                    timechange_0.2.0           
##  [67] foreach_1.5.2               fansi_1.0.4                
##  [69] data.table_1.14.8           ggtree_3.8.0               
##  [71] rhdf5_2.44.0                RSpectra_0.16-1            
##  [73] irlba_2.3.5.1               ggrastr_1.0.2              
##  [75] gridGraphics_0.5-1          commonmark_1.9.0           
##  [77] ellipsis_0.3.2              lazyeval_0.2.2             
##  [79] yaml_2.3.7                  survival_3.5-7             
##  [81] scattermore_1.2             crayon_1.5.2               
##  [83] RcppAnnoy_0.0.21            progressr_0.13.0           
##  [85] tweenr_2.0.2                later_1.3.1                
##  [87] Rgraphviz_2.44.0            ggridges_0.5.4             
##  [89] codetools_0.2-19            base64enc_0.1-3            
##  [91] GlobalOptions_0.1.2         KEGGREST_1.40.0            
##  [93] ggfittext_0.10.1            Rtsne_0.16                 
##  [95] shape_1.4.6                 estimability_1.4.1         
##  [97] foreign_0.8-85              pkgconfig_2.0.3            
##  [99] KEGGgraph_1.60.0            xml2_1.3.5                 
## [101] GenomicRanges_1.52.0        IRanges_2.34.1             
## [103] aplot_0.1.10                spatstat.sparse_3.0-2      
## [105] ape_5.7-1                   xtable_1.8-4               
## [107] car_3.1-2                   highr_0.10                 
## [109] plyr_1.8.8                  polylabelr_0.2.0           
## [111] httr_1.4.6                  tools_4.3.2                
## [113] globals_0.16.2              beeswarm_0.4.0             
## [115] htmlTable_2.4.1             checkmate_2.2.0            
## [117] nlme_3.1-163                HDO.db_0.99.1              
## [119] digest_0.6.33               numDeriv_2016.8-1.1        
## [121] furrr_0.3.1                 farver_2.1.1               
## [123] tzdb_0.4.0                  reshape2_1.4.4             
## [125] yulab.utils_0.0.6           rpart_4.1.21               
## [127] glue_1.6.2                  cachem_1.0.8               
## [129] polyclip_1.10-4             Hmisc_5.1-0                
## [131] generics_0.1.3              Biostrings_2.68.1          
## [133] stats4_4.3.2                mvtnorm_1.2-2              
## [135] parallelly_1.36.0           impute_1.74.1              
## [137] ScaledMatrix_1.8.1          carData_3.0-5              
## [139] minqa_1.2.5                 pbapply_1.7-2              
## [141] randomcoloR_1.1.0.1         SummarizedExperiment_1.30.2
## [143] vroom_1.6.3                 gson_0.1.0                 
## [145] utf8_1.2.3                  graphlayouts_1.0.0         
## [147] datawizard_0.8.0            preprocessCore_1.62.1      
## [149] ggsignif_0.6.4              shiny_1.7.4.1              
## [151] GenomeInfoDbData_1.2.10     rhdf5filters_1.12.1        
## [153] parameters_0.21.1           RCurl_1.98-1.12            
## [155] memoise_2.0.1               rmarkdown_2.23             
## [157] downloader_0.4              future_1.33.0              
## [159] RANN_2.6.1                  Cairo_1.6-1                
## [161] spatstat.data_3.0-1         rstudioapi_0.15.0          
## [163] cluster_2.1.4               janitor_2.2.0              
## [165] spatstat.utils_3.0-3        hms_1.1.3                  
## [167] fitdistrplus_1.1-11         munsell_0.5.0              
## [169] cowplot_1.1.1               colorspace_2.1-0           
## [171] ellipse_0.5.0               rlang_1.1.1                
## [173] GenomeInfoDb_1.36.1         DelayedMatrixStats_1.22.6  
## [175] sparseMatrixStats_1.12.2    ggforce_0.4.1              
## [177] mgcv_1.9-0                  xfun_0.39                  
## [179] coda_0.19-4                 iterators_1.0.14           
## [181] matrixStats_1.0.0           rARPACK_0.11-0             
## [183] abind_1.4-5                 GOSemSim_2.26.1            
## [185] treeio_1.25.2               Rhdf5lib_1.22.1            
## [187] bitops_1.0-7                promises_1.2.0.1           
## [189] scatterpie_0.2.1            RSQLite_2.3.1              
## [191] qvalue_2.32.0               fgsea_1.26.0               
## [193] DelayedArray_0.26.7         GO.db_3.17.0               
## [195] compiler_4.3.2              beachmat_2.16.0            
## [197] boot_1.3-28.1               listenv_0.9.0              
## [199] Rcpp_1.0.11                 BiocSingular_1.16.0        
## [201] tensor_1.5                  BiocParallel_1.34.2        
## [203] insight_0.19.3              gridtext_0.1.5             
## [205] spatstat.random_3.1-5       R6_2.5.1                   
## [207] fastmap_1.1.1               fastmatch_1.1-3            
## [209] rstatix_0.7.2               vipor_0.4.5                
## [211] ROCR_1.0-11                 rsvd_1.0.5                 
## [213] nnet_7.3-19                 gtable_0.3.3               
## [215] KernSmooth_2.23-22          miniUI_0.1.1.1             
## [217] deldir_1.0-9                htmltools_0.5.5            
## [219] bit64_4.0.5                 spatstat.explore_3.2-1     
## [221] lifecycle_1.0.3             nloptr_2.0.3               
## [223] sass_0.4.7                  vctrs_0.6.3                
## [225] spatstat.geom_3.2-4         snakecase_0.11.0           
## [227] DOSE_3.26.1                 ggfun_0.1.1                
## [229] sp_2.0-0                    future.apply_1.11.0        
## [231] bslib_0.5.0                 pillar_1.9.0               
## [233] magick_2.8.1                jsonlite_1.8.7             
## [235] markdown_1.7                GetoptLong_1.0.5